Level 4 Perks
Scoundrel Requirements: Cha 4 - Gives you five points in Speech and Barter. A very meh perk overall, due to the fact that barter is nearly useless. You're essentially spending a perk for 5 points in speech, and that isn't efficient.
Iron Fist Requirements: Str 3 - If you're going for an unarmed character, this is one of several perks that can make your surprisingly deadly. The additional 5 points of damage it adds is good, and even better when you consider you can stack this three times. That is 15 points of additional damage that you won't need to every buy ammo for.
Entomologist Requirements: Int 4 Science 40 - Increases damage against mutated insects by 50%. This is basically worthless, because mutated insects are almost without exception very easy to kill.
Educated Requirements: Int 4 - This increases the amount of skill points you gain per level by 3 if you have an average intelligence score. You should absolutely get this at level 4. Skills are important this allows you to level them up more than you would be able to otherwise.
Comprehension Requirements: Int 4 - Doubles the amount of skill points you receive from reading books, which means you get two skill points instead of one. This is much more useful than it sounds. The only flaw with this perk is that educated allows you decide exactly where your extra points are put, while Comprehension forces you to simply gain the skills available in whatever book you are reading. This is fairly large flaw, but if you're a skill-hog, take both Comprehension and Educated.
Child At Heart Requirements: Cha 4 - Gives you extra dialogue options with children. Sometimes interesting, but for the most part this isn't valuable.
Level 6 Perks
Bloody Mess Requirements: None - Makes your enemies explode in a burst of blood and gore. This is a lot of fun, and makes this a staple Fallout perk. You also do 5% more damage with all weapons, which isn't terribly useful.
Demolition Expert Requirements: Explosives 50 - With each rank of this, your explosives do 20% more damage. Since you can rank this up 3 times, you can gain up to 60% more damage with explosives. That is a lot. But the fact that explosives are heavy to carry around and not useful at long range remain limitations. If you're one of the few who actually use explosives routinely, then this is a must have, but for most people this can be passed by.
Fortune Finder Requirements: Luck 5 - Allows you to find more money than you would otherwise. Not very useful, because by level ten you'll probably be rolling in caps anyway.
Gunslinger Requirements: None - This increases your accuracy with pistols in VATS. However, pistols are one of the worst weapons in the game, so this isn't a useful perk.
Lead Belly Requirements: End 5 - This halves the amount of radiation you receive when drinking from radiated water sources. Since you probably don't do that very often, and Rad-away isn't that hard to come by, this perk is lackluster.
Toughness Requirements: End 5 - Increases your damage resistance by to 10% to a maximum of 85%. It sounds good, but there is a problem - the game isn't very clear about how the DR rating on a set of armor translates into a percentage. That said, a dead character does nothing so this is probably worth taking.
Fallout 3 Perk Guide
Fallout 3 is a complex game, with choices that will challenge you throughout your life in the Wasteland. One of these choices is your Perks - the abilities that make you more powerful than the average survivor. This guide will help you choose the best Perks, so you can not only survive, but thrive.