I've only found 2 bobbleheads to date - 1 right at the start of the game in Vault 101 for medicine and the 2nd was the agility one.
I think the next playthrough I'll forgo big guns and not take the gun nut perk, instead replacing it with a couple of levels of intense training. Fatman aside, small guns and energy weapons are proving to be far more useful, even if the ammo for energy stuff is rare early on.
The same guy who posted the character creation tips I reposted earlier has now given his opinions on the various perks:
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Well, I went to (a Nyquil induced) sleep really early last night as I've got a nasty case of bronchitis, and I'm up now, I figure I might as well keep myself busy and provide interested folks with a list of the perks and (in my view) their relative worth from 1 to 10, with 10 being a true 'must have' perk.
So:
Level 2 Perks
Black Widow/Lady Killer (7/3): There are more male characters who you can have more of an effect on with the BW perk if you're a woman, but the solutions you get can often be worked around, anyway. There are also more male enemies than female, so it does make some sense as a combat perk for women. Not so much for men. I wouldn't advise taking the LK perk, as there just aren't enough opportunities to really make use of it.
Daddy's Boy/Daddy's Girl (1): Taking perks to improve skills is a waste of a perfectly good perk unless you absolutely need those skillpoints and are already a high level. In general, don't waste the perk since you should be able to bring up any skill, at all, to level 100 within 4 levels as maximum.
Gun Nut (1): a skill raising perk.
Intense Training (8): this is the perk that'll allow you to 'undo' some of the min/maxing I suggested in one of my previous posts. It allows you to start with 10 points in intelligence and to level up perception and agility to 10 as well. If you level up and can't think of a perk to slot in, consider raising luck or endurance a bit.
Little Leaguer (1): a skill raising perk.
Swift Learner (3): it has some use if you plan on only playing through the main quest line (still, you should probably get to level 15 or 16 without this perk). If you plan on exploring the wasteland, however, you just don't need this perk. You'll cap out at the level 20 level cap anyways just fine without it.
Thief (1): a skill raising perk.
Level 4 Perks.
Child at Heart(3): there are some uses for this perk and it'll give you some interesting dialog choices with a few otherwise recalcitrant children in the game. Still, it's not really worth the investment of a perk slot unless you've already beaten the game once and just want to see some other possible dialog arcs.
Comprehension (6): this can be a very useful perk, especially if you're at a lower level and finding a bunch of skill books as there really are a lot of them in the game. Still, this probably shouldn't be a necessary perk and you can get you main skills up to 100, without this, with no problem.
Educated (8): this is an awesome perk. By the time you reach level 20, you will have earned an extra 48 skillpoints from this. And unlike all the normal skill raising perks, you can devote those points wherever you feel like.
Entomologist (2): Yes, there are lots of giant bugs in the wasteland. But other than the giant radscorpions and some of the giant ants (especially the fire breathing ones), none should give you any trouble once you really get your character started.
Iron Fist (5): with three available ranks, you can end up doing an extra 15 points of damage with every unarmed strike. Of course as ranged combat is far superior to melee combat in this game, you should only consider taking this perk if you're on the path to becoming the wasteland's Bruce Lee.
Scoundrel (2): Not just a normal skill raising perk, this does give a few extra dialog options through the game. Still, not really worth taking.
Level 6 Perks
Bloody Mess (7): Okay, I love gore and the spectacular death animations. The 5% bonus to all damage types is also pretty cool.
Demolition Expert (9): going to be using lots of mines or grenades? Put three ranks into this skill. If not, consider it totally worthless.
Fortune Finder (1): by the time you really get rolling, you'll have more caps than you can spend. Ignore this perk.
Gunslinger: (3): an interesting perk, but the best and most plentiful small guns in the game are two handed. A sidearm should be your holdout weapon that you use if your primary breaks or if you need to conserve your main type of ammo. Even the SMG, while nifty, eats up ammo too quickly and really isn't an improvement over an assault rifle.
Lead Belly (2): you drinking much irradiated water? No, probably not. Besides, 100 caps will buy you a radiation detox at a doctor and there is plenty of rad away to be found. If you don't plan on gargling with random sink water, don't take this perk.
Toughness (4) : a 10% increased damage resistance is kinda nice ,especially since it stacks with other bonuses. Don't rely on it, though. But do consider taking it if you have a free perk slot and nothing else appeals to you.
Level 8 Perks
Commando (8): two handed weapons are awesome, and any increase in VATS % is good. If you use rifles, take this perk.
Impartial Mediation (2): only take this perk if you don't plan on getting speech to 100 anyways. And even then, only take it if, somehow, you won't be either good or evil.
Rad Resistance (5) : an extra 25% to your rad resist? Excellent. This, along with the bonuses for completing the Wasteland Survival Guide and getting the Food Sanitizer should allow you to go much longer without needing to remove your rad levels. It also gives you a much greater effect from anti-rad apparel since this bonus will stack.
Scrounger (6): if you're the type to run short on ammo, take this perk without a second thought. Once you've played through the game and are used to its combat mechanics, though, you won't need to bother with this and you should have more than enough ammo.
Size Matters (1) : a skill raising perk.
Strong Back (4): I personally love this perk, as it's got the same effect as raising your strength by 5 full points, and I like to carry loads of junk around.
Level 10 Perks
Animal Friend (2): eh, it's okay. It's good that it works on the Yao Guai, but since it doesn't effect Deathclaws, it's pretty much useless for the kind of enemies you'd actually need it for. Most cases, though, animals simply won't do enough damage to you or be important enough in a fight that their switching sides would really matter.
Finesse (9): an effective 5 point bump in your luck stat for critical hits? Unless you were silly enough to bump your base luck stat up past 5, definitely take this perk. Even then, probably take it anyway.
Here and Now (-10): yes, negative ten. You just leveled up, the main bonus to leveling up is that you can raise your skills, and choose a perk. Why throw away a perk just so you can level up again? Only take this if you're just playing the main quest, and even then, only if you decided against the EXP increasing perk.
Mister Sandman (3): there aren't many sleeping enemies that you'll come across, but there are a few. Even then, you need a very high sneak skill to get up to them without waking them. Still, if you're going for the unarmed route, consider getting this simply to add flavor to your character.
Mysterious Stranger (3): by the time you're really rolling, you should be able to kill almost any single enemy in VATS mode. However, if you're having trouble with some really big bad monsters (like Super Mutant Masters) then having the ability to finish them off in a single VATS phase, especially if you have the Grim Reaper perk, is probably going to be worth your while.
Nerd Rage! (3): the 50% damage resistance is nice if you're already in serious trouble. Then again, if you're already in serious trouble the 50% damage resistance boost won't really help all that much and you'll want to shoot up with some stimpacks asap anyway.
Night Person (1): you should have intelligence at 10 from character creation on, and you should max out perception before you really invest in energy weapons anyways. Ignore this perk.
Level 12 Perks
Cannibal (4): there are lots of corpses, and so this is an easy way to get lots of health back. However, you shouldn't really need to eat corpses as, in most cases, there is a bed around somewhere or you can just fast travel back to whichever home/apartment you own. Also don't even think of taking this perk unless you're going for the 'evil' side of things.
Fast Metabolism (3): it's useful to get an extra boost out of stims, and you should consider taking this perk during your first play through if you find yourself running low on (or out of) stims. Otherwise, don't bother. You'll only need to rely on stims for major firefights and even then you should have more than enough to keep you drugged up.
Life Giver (2): extra HP are nice. But this amounts to a tiny bump in extra HP and isn't really worth the investment.
Pyromaniac (7): using the flamer or skishkebab? Take this perk. Not using them? Ignore it.
Robotics Expert (8): this perk can actually be pretty useful if you have a good sneak ability. There are enough robots in the game to justify the damage bonus and enough times when taking out a mechanical angel of death makes sense. Still, if you find yourself blowing away most robots without trouble, or if your sneak is low, don't take a second glance at this perk.
Silent Running (8): the skillpoint raise is a wash, but the ability to run while sneaking and not lower your sneak chances is pretty neat. If you plan on taking this, don't level your sneak skill up higher than 80, as you'll get a bobblehead and then this perk to bring it to 100.
Sniper (10): a significant increase in your chance to pull off headshots in VATS, regardless of what weapons you're using. Get it.
Level 14 Perks
Adamantium Skeleton (3): if you're often ending up with crippled limbs (generally from a mine/grenade) then this perk is worth it. Probably, though, it aint.
Chemist: (2): useful if you rely on chems. You shouldn't have to though, and you should generally have enough in your inventory to simply shoot up again once they wear off, anyway.
Contract Killer (2): if you're evil and could use some extra caps, take this perk. However, most enemies you fight will be evil, so you'll really have to go out of your way to make use of this perk much (like depopulating Megaton or something).
Cyborg (8): actually a pretty good perk. You get a good bonus to several of your resists and an extra 10 point buff to your energy weapons skill.
Lawbringer (4): if you're good and could use some extra caps, take this perk.
Light Step (2): you're setting off traps? Really? Just use the save-load magic spell (or the load-save magic spell) and you should be fine. Take this if you can't be bothered to pay much attention and prefer being able to just concentrate on run and gun combat.
Master Trader (1): a skill raising perk, and one which raises a skill that you probably shouldn't really need in the first place. You should be able to find all the armor, weapons, ammo and chems that you could possibly ever use.
Level 16 Perks
Action Boy (10): use VATS? Take this perk.
Better Criticals (4): most enemies will be dead if you get a critical or two during a VATS chain, anyways. If not, then this perk might come in handy. But even then, you won't be doing all that many criticals in the first place. The only (major!) exception to this is that you always manage a critical hit if you attack while successfully sneaking. So if you have lots of points in sneak and are fighting big bad monsters, invest in this.
Chem Resistant (4): take lots of chems and don't want to be bothered with beating the addictions? Then this is worth it. Don't bother with chems (as you probably shouldn't?), don't bother with this perk either.
Tag! (1): oooooh, a skill raising perk. Yay!
Level 18 Perks
Concentrated Fire (3): eh. Chances are, you'll already be hitting in VATS often enough if you take the right perks. A slight increase in accuracy for low % hits probably isn't worth it.
Computer Whiz (-10): yes, another negative 10. First of all, you can meta-game and simply save-load. Second of all, you can just abuse game mechanics, since every single computer terminal in the game allows you three free attempts, and then you can log off and back in to get another three free attempts. Ad infinitum.
Infiltrator (2): if you force a lot of locks, take this, I guess. Otherwise, just use save-load or be a bit careful in your lockpicking.
Paralyzing Palm (3): paralyzing enemies is good. Having to fight totally unarmed is bad. Unless you have your heart set on unarmed combat, fuck this perk.
Level 20 Perks
Explorer (10): this is an awesome perk, and if you want to fully explore the wasteland you really should consider picking it up. However, if combat is more important to you, don't consider this perk for a second, because GRS is a hell of a lot better.
Grim Reaper's Spirit (over 9000!): the single best perk in the game, it turns you into a one man meat packing factory. Target an enemy, spend all your AP's to blow their head off, and immediately get all your AP's back to do it again.
Ninja (9): went the unarmed/melee route? Take this perk.
Solar Powered. (2): this is a level 20 perk? On purpose? To begin with, the heal rate is simply too slow to really make use of. Stimpacks/food will often do just as good if not better, this doesn't heal crippled limbs, doesn't work inside buildings and takes up a highly valuable level 20 perk slot. Of which you get only 1.