Perks I rather doubt the usefulness of:
Bonus HtH Damage (3): Should have been a lot more damage. Now you'll have to get all three levels to notice any difference. Note that this perk only adds to the maximum damage - that's only one point on average for each perk slot!
Bonus Ranged Damage (2): Not nearly enough of a bonus unless you're using a Minigun.
Explorer: Improves your chances of finding special encounters, which is good at low LK but seems a bit vague. Could have been OK at level 6.
Lifegiver (2): Once you reach level 12 your maximum number of Hit Points won't be so important any more, and there aren't too many levels to go anyway.
Pickpocket: Neat for thief characters, I suppose. But if you fail at stealing, won't you just quickload?
Silent Death: Guess which one of this and Slayer you should choose at level 18. Then after eventually reaching level 21, you'd want to put skill points in Sneak to make one of your attacks do double damage? I laugh hard!
Silent Running: If you must play a sneaking character I suppose this takes a lot of frustration out of playing, but doesn't it spoil the atmosphere? A convenience perk.
Smooth Talker (3): The closest thing to Gain Intelligence in this game, but I'd start with a good IN instead.
Strong Back (3): Carrying more stuff can't be wrong, but spending perks to do it is. Especially if you have an NPC.
a green star The Lifegiver perk gives you 4 extra HP for each new level in addition to the 4 HP you get just for taking the perk (the manual forgets to say this, but it's in the patch notes).
a green star It's possible to score more than one double-damage hit with Silent Death in the first round of combat, assuming you can position yourself behind two or more enemies without leaving Sneak mode (which is difficult if you have to pass directly in front of them).
Useless perks which should only be chosen if you have no other options (or really want to):
Animal Friend: Well, how useful is this.
Cult of Personality, Presence (3): The potential benefits of these perks are frighteningly small.
Earlier Sequence (3): Not worth it.
Educated (3), Master Thief, Medic, Mr. Fixit, Speaker: All these perks give you nothing but skill points. You don't need more skill points. You need perks. As for Educated, if you get it at level 6 and then level up ten times, you've gained 20 skill points. Over time. Some guide writers recommend it.
Empathy: It seems like a great idea in theory, but this game simply isn't about choosing the dialogue options that keep other people happy.
Faster Healing (3), Healer (3): Healing rate is never an issue.
Flower Child: Convenient for a chem character. But using chems sucks.
Fortune Finder, Master Trader: Money is not an issue. Fortune Finder is simply awful; Master Trader isn't actively bad, just strictly unnecessary.
Friendly Foe: Noooo. This is free in Fallout 2, as of course it should be.
Ghost: Like a skill point perk only you don't get the skill points!
Heave Ho!: Strictly for grenade chums, and exceptionally marginal even so.
Mental Block: There's no need for this at all.
Mutate!: Don't waste a perk changing traits in mid-game instead of choosing right to begin with. (Well, it would be OK to change Finesse into Fast Shot at level 21 after getting Sniper and having a high LK, but if you get to that point you're not playing a regular game anyway.)
Mysterious Stranger: Utterly useless.
Night Vision (3): Situational, and doesn't do much. Increase your weapon skill instead, or even pick Sharpshooter.
Pathfinder (2): Time is not an issue... er, well, maybe it is, but not this important!
Rad Resistance (3), Snakeater: Poison and radiation aren't common enough, or difficult enough to handle, to necessitate these small bonuses.
Ranger (3): Random encounters aren't that bothersome.
Scout: Pointless.
Scrounger: You don't need this.
Sharpshooter (2): Effectively just a minimal skill increase for ranged attacks. Raise your preferred weapon skill instead and use the perk for something special.
Survivalist (3): Look! If you take all three levels of this perk it will make it virtually impossible for you to get caught in a rock slide when travelling and get hit for 2 points of damage! It is a must!
Swift Learner (3): This helps you gain levels. What's the primary purpose of gaining levels? To get perks. So why use perks to gain more levels?
a green star The effective size of the discount granted by Master Trader varies between shops, roughly in a 15-30% range. This is probably because barter modifiers are applied cumulatively and not sequentially.
a green star If you have only one trait when you get the Mutate! perk, you must exchange that for the new one, i.e. you can't just fill the other slot and keep the old trait.
a red star In v1.0 you could reportedly use Mutate! to change Gifted into something else but still keep the stat points.
a green star The effect of Night Vision varies depending on the lighting conditions and your number of perk levels. Each modifier threshold you cross gives you +15% to hit with a ranged weapon, for a maximum of +30% in complete darkness with three levels of Night Vision. At other times, any specific level might not do anything at all. Frank Shannon notes that Night Vision adds some clarity for people with dark monitors.
a green star Sharpshooter is bugged and doesn't really do what the manual says; it's supposed to raise PE by 2 for sniping purposes, yet often improves your chance to hit less, and never more, than increasing PE by 1. Michal Burger figured out that this is because the perk thinks range modifiers are calculated based on PE when it's in fact PE*2, and so increases your chance to hit only half as much as it should. At least it gives you a bonus even if your PE is at 10 already.
a green star Swift Learner is even worse here than in Fallout 2, since you can't go beyond level 21. It may seem like a good investment when you first look at it, but since the xp requirement for each new level rises linearly, even if you get all three slots of Swift Learner you only ever stay at most one level ahead of someone who doesn't ruin their early game wasting invaluable perks, and for that you'll have to wait until level 17! So, that adds up eventually to a few HP and skill points, for three perks... Do not choose this perk ever, ever, ever, ever!
Looks like I'll be rolling my next few characters without Awareness...
But these kind of things are debatable because people would probably bitch that it became broken or something. [Then again, that's what we have optional checkboxes in installers for 
]
