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The easiest thing to forget about when planning which perks you intend to take are the requirements needed to be eligible for a perk. This is because early perks don't have very strict requirements, and so early into the game you will see most perks show up. At later stages however, many perks have strict requirements. Take Cyborg, for instance. It is a good combat perk, but to take it, you need 60 skill points in both Medicine and Science. Unless you were planning with those requirements in mind, it is likely that a combat oriented-character would not be able to take the Cyborg perk.
If you want an optimal character, you should pick a few important perks - the ones you feel are really critical to the success of your character - and plan out your skills so that you don't miss a perk that you really want because you didn't have the requirements. You need to be extra careful with powerful higher-level perks as well, because - unlike lower level perks - you won't be getting many chances to pick a missed high-level perk up if you happen to lack the requirements for it when you level up.
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Stacking Perks, Skills, and Attributes
One rule that you should always stick to when taking perks is to use them to help maximum advantages you already have. Taking a few combat perks and a few stealth perks and a few non-combat perks probably won't result in an outstanding character. This is both because stacking perk effects allows you to be incredibly powerful in a certain area, and because you'll ultimately need to give your skills and attributes a clear focus in order to qualify for the best high-level perks. For example, the level 20 perk Ninja requires 80 points in Sneak and 80 points in Melee weapons. If you're going to take that perk, you might as well design your entire character to be focused on melee combat and stealth. And if you plan to take Ninja, that you might as well take Silent Running. And if you're focusing on combat and sneak attacks, you probably want to take perks which increase your crit chance and your crit damage. As in most games, specialization is key.
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The Value Of Skill Perks
There are many perks in Fallout 3 which simply increase one or two skills. On paper, these perks simply look like places where the developers ran out of good idea. But in use, these perks are very important to your character's development. Not all perks are worth taking, and even less perks are worth taking for a certain kind of character. Someone who uses Small Guns won't be interested in perks that increase Energy Weapons, and a stealth character probably won't be interested in perks that increase health and survivability, instead choosing ones that increase damage.
As a result, you'll probably find many levels where none of the perks look tempting. If that is the case, then skill-increasing perks are a great choice, because by taking them you increase the overall pool of skill points that your character has. There is no benefit to increasing a skill past 100, so skill points gained by perks gives you additional skill points to put elsewhere. Now obviously you don't want to take a skill perk if you have absolutely no use for the skill in question. The perk that increases Barter and Speech skills is a good example of this - Barter is always worthless, so that skill perk is terrible. However, as long as the skill perk provides points in a skill you plan to use either immediately or in the future, it is a great investment. Take Size Matters, for example. Using that perk, you gain 15 skill points in Big Guns. As long as you intend to use Big Guns, that is a wonderful perk. It means that you have gained an additional level of skill points overall, provided your character is of average intelligence and would typically gain 15 skill points from gaining a level. Those 15 skill points can be put somewhere else, like Science or Speech, resulting in a character with more well-rounded skills.
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Go Forth To Glory!
Watch out for yourself in the Wasteland. It is never an easy place to get along, but with this information in hand you should be able to give yourself an edge. Remember to specialize, remember to stack your benefits, and if you run across a perk that you are unsure about, always check the guide first. But more importantly than any of that, remember to have a plan. Nothing is worse than building a character focused on a particular style of play, only to find the best high-level perk for that style is out of reach because you didn't remember the requirements needed to qualify for it. If you're not sure about what is needed, consult this guide or your manual.