Nonlethal Damage

Core

It's actually quite simple to do this. In the SRD, you'll see a rule that allows you to deal nonlethal damage with any weapon that normally deals lethal damage:

Nonlethal Damage with a Weapon that Deals Lethal Damage

You can use a melee weapon that deals lethal damage to deal nonlethal damage instead, but you take a –4 penalty on your attack

... which makes sense. You have to take much more care not to kill someone with a sword and just knock them out. But the option is there for you! And it makes for very cool character fluff, in my opinion.

Also, as @GMJoe kindly pointed out, there is a core enchantment in the 3.5 Dungeon Master's Guide (pg. 225) called Merciful for only a +1 bonus. You'll certainly want this (assuming you don't use one of the weapons which already deals nonlethal damage):

The weapon deals an extra 1d6 points of damage, and all damage it deals is nonlethal damage. On command, the weapon suppresses this ability until commanded to resume it. Bows, crossbows, and slings so crafted bestow the merciful effect upon their ammunition.

Other Source Books

The best sources for nonlethal damage in books outside of core come from the Book of Exalted Deeds:

• pg. 34, Nonlethal Weapons: Contains, as you might expect, a broader range of weapons which only inflict nonlethal damage. Can be upgraded per the normal magic item rules and you don't need to take the -4 attack bonus associated with the above rule. Includes...
  • Truncheon: 1d8 nonlethal, bludgeoning, martial, one-handed melee weapon
  • Entangling Pole: 1d4 nonlethal, piercing, exotic, two-handed melee weapon
  • Grasping Pole: 1d4 nonlethal, bludgeoning, exotic, two-handed melee weapon
  • Lasso (yee-haw!): special, --, ranged weapon (10 ft.)
• pg. 40, Feats: There are a couple of feats which will allow you to deal nonlethal damage more effectively. Again, all of these come at the cost of the feat, so they will still essentially make you less effective than someone doing lethal damage (who at least has one feat up on you).
  • Subduing Strike: No penalty when dealing nonlethal damage; rogue’s sneak attack deals nonlethal damage
  • Holy Subdual: Transform bonus and smite damage to nonlethal
  • Nonlethal Substitution: Transform spell’s energy damage to nonlethal
  • Vow of Nonviolence: +4 to spell DC if it does not deal real damage
  • Vow of Peace: calm emotions aura, +2 natural AC, +2 deflection AC, +2 exalted AC, some normal weapons shatter when they contact you, +4 Diplomacy

Optimal Build (?)

So, really, it looks like your best bet would be to become a traditional, overpowered spellcaster, take the Nonlethal Substitution feat (which will allow you to use your spells to deal nonlethal damage), then use the various Vow feats to increase your other statistics. That looks like maximum leverage to me. I don't know of any other source books that would really contribute much to this effort.

Addendum

As far as dealing more damage than a normal damage dealer, that is likely next to impossible without being very, very creative. For starters, there just aren't that many sources of nonlethal damage in the core rules. If you look in the Environment section, it might be possible for you to make some homebrew rules with your DM based on these (i.e., cold effects which numb instead of kill). If you want to stay strictly within the RAW, though, I think your best bet for having a highly functioning nonlethal character would be to have a spellcaster of some kind who only utilizes sleep spells, hold person spells, and the like. I didn't include this in the main answer because these effects don't technically deal damage, but it's an option which may appeal to you.

No, it does not.

All that Improved Uncanny Dodge does is this:

A rogue of 8th level or higher can no longer be flanked.

In particular, it does not make you immune to sneak attacks (if you lose your Dex to AC from some other way you can still be sneak attacked, for example).

The fact that they are both precision damage, or that the parent class is rogue doesn't do anything here since Improved Uncanny Dodge does not care about that.