I was once feeling just like you feel. There seem to be so many choices and with 250 perks and a max of 80 perk points you will always feel like you are missing out on something. So, this is just a list of pointers to try and make you feel more comfortable because at the end of the day, you will find you have more than enough perk points as you can not cast a spell, shoot a bow and backstab all at once, you will generally be finding yourself doing one of those most of the time.
- Gear and Crafting Perks
- The best armor and weapons in the game are player crafted.
- Any suit of armor, light or heavy (not robes) can be crafted up to the effective armor cap of 567 granting 80% damage reduction (Yes, even hide armor if you are patient enough).
- The best weapons are Deadric, but glass is fairly close behind them. If you want the best weapons but are using light armor, you will want to go up the Heavy armor side of the tree as this will grant you access to daedric weapons but also dragon armor, the best base defense light armor in the game.
- Armor perks are almost a waste Unless you are trying to cap out armors like Hide or Iron. For instance, my first attempt at making a very nice suit of Dragonscale armor left me with a suit that had 1157 armor rating, almost 600 over the cap. This caused me to restart my character and ignore armor perks this time around completely (makes it a bit more challenging until you get a nice suit of armor. I suggest joining the Thieves Guild or Dark Brotherhood to get their suits as it is fairly quick/easy to do).
- Useful skill trees, that if you are going to be using them, where almost all the perks are of use.
- Destruction - Especially Impact, pretty much all the skills here are worth it as you can not find one element that is equally effective against all enemies.
- Archery - Just has some additional abilities that make you more effective at all ranges
- Sneak - If you just want the initial damage then just go up the right side. If you are a stealth fighter however you will want both the left and the right sides of this branch.
- Enchanting and Smithing - While you can do very well with just items you find in game, these skills are an excellent source of income as well as the best weapons and armor in the game that are also tailored specifically to your needs.
- Partial Tree Suggestions
- Alchemy - I go with the base perk and then up high enough to get the extra bonuses to potions and poisons but no higher. This will really give you the maximum effectiveness out of your potions (and worth, this is probably the easiest money maker just because of the number of merchants who will buy potions and the relatively low weight to carry them around).
- Conjuration - At high levels your summons will already be permenant (These are the Thrall spells) so you will not be actively casting and recasting these spells. All you will need to do is be able to cast the spell when your summons die to bring them back.
- Restoration - I just get the Novice ability here and have never had a problem using this to heal after a battle (or some times during but usually potions are much more useful). If you are going to be a magic type with out wanting to use robes, consider the Magic Regen perks as well, they are not too far down the tree.
- Armor Skills - As mentioned, one point in the base skill is all you need to craft a suit of any type of armor to the effective armor level cap.
- Useful skills with useless perks
- Pick pocketing - I usually get this skill to 100 before any other, but the perks just do not add much to this besides novelty. The extra carrying capacity is worth noting but I tend to play high stamina characters (I can carry around 400 units regardless of character type)
- Lock Picking - I pick everything but never put a point into this tree. If I get a key for a door that does not require it I usually stash the key, pick the door then get the key (as I like collecting them :))
- Speech - I love raising the skill for the better bonuses but I can not justify a perk in this branch just to make selling things easier. At the end of the day its not worth a perk to stop me from fast traveling from town to town to town to sell off all that I have (And if you ever become interested in the thieves guild, you will not even have to travel that much!) NOTE: If you are playing a character that will not fast travel (I have one of these) A few points in Barter has made more effective use of the shops near by. However, once you start crafting things like Banish daggers, the price of them is enough to wipe out any merchant's reserves with just a single dagger.
So I hope that is enough generic information touching lightly or indepth on just about every skill. If you have any more specifics you want to know there is alot of information on here about specific builds and usefulness of different perks and such.
EDIT: Below is a good comment worth putting into this answer in regards to the Dawnguard DLC.
With Dawnguard, you can now smith Dragonbone weapons. This makes speacializing in Light Armor and going up the left side of the Smithing tree a viable option, while still maintaining the ability to use the best weapons in the game. Dragonbone weapons have slightly higher base stats than Daedric, so the smithed ones should be correspondingly better too. I think the bullet point starting with "The best weapons are Deadric" should be removed from the answer. – rkagerer