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Survival of the Skillful
Bethesda's masterpieces have all featured similar character development, and although Fallout 3 makes larger modifications to leveling than any game Bethesda has put out to date, there are still some core mechanics that remain the same. The most important of these are Skills, which represent your ability to perform various tasks in the wasteland. Each skill is required to perform a certain task, and if you have a low level of skill, you may not be able to perform the task at all. For example, having a low Science skill will prevent you from even attempting to hack computers.
But not all Skills are created equal. Some are more situational than others, which means that you can pass them over if you're willing to deal with the fact you may encounter road-blocks that you cannot get past because you don't have the proper skills.
For starter's, it is best to familiarize yourself with what each skill does. And while we're at it, I'm going to throw in my opinion about the usefulness of each skill.
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Barter (Charisma): Putting points into Barter will cause traders to give you more money for your stuff, while you'll have to pay less for theirs. Don't bother with it. You may start dirt pour, but you'll be plenty rich by the time you're level ten.
Big Guns (Endurance): This skill is obvious - it determines how well you can use Big Guns. Big Guns are good weapons for clearing out packs of enemies. However, ammo for them is extremely expensive and fairly rare, so I don't recommend taking this as your primary form of offense.
Energy Weapons (Perception): Affects how you use lasers guns and such. Energy weapons are powerful and ammo is plentiful throughout, but that also tends to be true of Small Guns as well. I suggest you pick whatever better fits your attributes.
Explosives (Perception): Determines the power of mines and explosives. Nice, but you probably won't use these items enough to get the most out of this skill.
Lockpick (Perception): Lets you pick locks, of course. This skill is required to access certain areas of the game, and if you don't have a high enough skill, your only real hope is to maybe bump it up using Mentats. Level this skill if getting past locked doors if important to you, otherwise forget it.
Medicine (Intelligence): Gives you more bang-for-your-buck from medicines. Useful for nearly every character, though you don't have to max it out.
Melee Weapons (Strength): Turns you into a swordmaster. Or a psycho with a sledgehammer. Melee weapons can be very powerful, but you also have to be in your opponent's face. A good choice for high-endurance characters.
Repair (Intelligence): Allows you to fix your weapons. Very useful, not only because of the cash savings, but also because you can spend more time in the Wasteland before going back to Megaton or Rivet City for a resupply.
Science (Intelligence): Allows you to hack computers. Like Lockpick, there are certain things in the game you simply won't be able to access without this skill. Also lets you hack turrents and use them against enemies.
Small Guns (Agility): Not nearly as puny as the "Small" might make you believe, as this includes shotguns, sniper rifles, and machine guns. This is a good choice for a bread-and-butter combat skill. Don't level this if you're leveling Energy Weapons.
Sneak (Agility): Allows you to pass undetected, and perform very powerful sneak attacks. This skill is absolutely murderous at high levels, and nearly useless if kept low, so make sure you're fully committed once you start dumping points into it.
Speech (Charisma): With this skill, you can sweet-talk many of Fallout's characters. There are quite a few interesting quests and dialogue choices that are only viable if you dump points into this skill.
Unarmed (Endurance): Lets you beat down your enemy with your bare hands. This can be fairly effective, but isn't as powerful overall as the gun skills. Good as a secondary skill, in case you are low on ammo.
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Like most games, the skills in Fallout 3 tend to work best if you choose a few areas to specialize in. Keep in mind that skills are associated with attributes, so you'll have an easier time maxing out skills that are associated with attributes in which you excel.
You'll want to have at least one bread-and-butter combat skill. This will be either Small Guns, Energy Weapons, or Melee Weapons. One is just as effective as the others, though Melee Weapons will require you to get up close, and you'll have to be a bit more careful to make sure that happens. If you're a real min-maxer, then remember that Small Guns is associated with Agility, and if you boost Agility you'll not only increase your combat skills but also your action points for use in VATS. Also keep in mind that most powered armors will give you an Agility penalty, but no such penalty exists for Perception.
When it comes to skills like Speech, Lockpick, and Science, I suggest either maxing them out or ignoring them. The really interesting and profitable things that can be accessed with these skills will require you to be highly proficient in them. There aren't many interesting things to be found in safes that are of merely "Average" difficulty, for example.
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Coordinating Skills with Perks and Items
If you read the manual, you probably realized that a lot of Perks that are available also increase skills. Some of these Perks increase skills so much that it seems inadvisable to actually invest many skill points into a skill. The most obvious example is Size Matters, which boosts your Big Guns skills by a full fifteen points. If you're focusing on Big Guns anyway, then taking this Perk effectively doubles the amount of skill points you are given for the level, assuming you have average intelligence and would normally gain fifteen skill points.
In the long run, using Perks for skills can be very effective, due to the relative weakness of many Perks and the fact that not all Perks are going to be relevant to the way you're building your character.
Also remember that Items which increase your skills beyond 100 aren't going to give you any additional benefit. If you plan on always using an item that gives you an extra five points in Science, for example, don't increase the base skill beyond 95.
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Rounding It Out
The most important advice I can give regarding skills is this: Have A Plan. If you don't have a plan, then you will waste your points as you decide to shape your character in one direction, and then change to focus on some other aspect. In fact, you should have a good idea of who your character will grow to be before you start the game. It is critical that you put at least five points into your main combat skill every level, and it is also important that you level up your favorite non-combat skills with similar aggressiveness. Maxing your lockpick skill out won't do you that much good if you're already 50 hours into the game, unless you feel like revisiting every locked safe you couldn't unlock because your skill was to low.
Specialize, plan, and survive. Good luck in the Wasteland!