My idea of of 'best rogue you can be' means being the best at the iconic rogue- ie: the abilities listed in the PHB- so I'll advise towards maximizing those.
Since the rogue's weapon proficiencies tend toward light damage, finessable weapons, your damage in a fight fight mainly comes from sneak attack. With that in mind, since your actual weapon doesn't matter as much then the loss of damage dice from a smaller weapon doesn't affect a rogue as much as it would a fighter. In other words, play a small character. You gain bonuses to hide, attack and ac -things every rogue needs and lose nothing, except carrying capacity which is fixed by picking up a bag of holding type item- something every rogue wants anyway!
One of the best small races for a rogue is the almost-broken whisper gnome (Races of Stone). Good stat bonuses, 30 ft movement even though they're small, both low light and darkvision, racial bonuses to sneaking/perception AND SLA's that are ludicrously perfect for a rogue. Like I said they're almost broken but they're not an ECL by the rules so they should be fine for an "anything you can find" type of DM. If you feel it's too cheesy though, the generic halfling is pretty good also. Or the Strongheart Halfling from Forgotten Realms. They lose the +1 to saves but gain a bonus feat- which will be handy considering...
FEATS
Since you'll have a low strength, high dex and finessable weapons the weapon finesse feat can be useful to have.
Since your relying on sneak attacks getting as many in as possible can be good also, so you might look at the two-weapon fighting feats.
There's also the problem of getting into position for sneak attacks, if you're worried about AoOs you could get the mobility feat. The dodge pre-req doesn't hurt and the spring attack follow-up is good for ultimate safety and good sneak attack hit-and-runs.
Finally, improved initiative is always good for rogues since going first is an excellent way to get in more sneak attacks.
Now that you're feat starved you might see if your DM allows flaws, a UA variant rule that lets you give your character penalties in exchange for feats. Since it's easy to take flaws which have little impact on your character be careful with this because it can get really cheesy- just how cheesy depends on your conscious and gaming ethic. At any rate, flaws can be use non-abusively. Shaky and non-combative are good ones depending on your intended combat style. Shaky gives you a -2 to ranged combat, non-combative a -2 to melee combat. Whichever one you take this is a flaw that
will affect your character. I'd suggest shaky simply to emphasize melee over ranged combat- you can't flank with ranged combat and flanking is essential for maximizing sneak attacks. You could also just cheese it up and take a flaw like light-sensitivity (from Dragon magazine #328- you have to have darkvision, you get dazzled in bright light or sunlight) which can be completely offset by spending 10 gp on sundark goggles (Races of the Dragon). Like I said, you can go as far with these as your gaming ethics, and your dm, will allow.
Of course there's more to rogue's than sneak attack...
SKILLS
Make sure you have a decent INT, because those high rogue skill points will never go as far as you'd like them to. The d20 system basically allows you to have as many maxed out skills as you have skill points per level. Since the skill roles of a rogue emphasize maxed out skills over dabbling (ie: a rogue usually can't afford to fail a skill check) you just need to figure out how many skill roles you want to fill. Chances are it's more than eight.
Keep in mind the skills which have static DCs (balance, climb, etc.) and those that are opposed (spot, listen, bluff, etc.). You'll always want to max out opposed check skills, since those DCs will scale with your level, but static DCs might have cut off points where you feel you've put in enough skill points for success. For instance, the "max DC" (assuming no situational modifiers or penalties) for a climb check is 30 for a slippery, natural wall or overhang. Assuming an 18 DEX (+4), a climbing kit (+2) and average rolls (10 or 11) you'd need at least 14 ranks in climb to succeed. So, theoretically, you could stop putting ranks in climb at 11th level- at which point you'll most likely have access to magic which renders actual climbing a moot point anyway.
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Use Magic Device deserves special mention since it allows you to serve as a secondary caster if you have the items to do it. Wands of Lesser Vigor are the best bang for the buck healing-wise and the DC 20 on UMD to use them when the cleric is unavailable (or the one that needs the healing) makes the skill point investment worth it. And that's just one low-level (and thus fairly cheap) wand that can really come in handy. Take a look at the spell lists and you'll find several other 1st, 2nd and even 0-level spells that could be highly useful in wand form for a rogue with just a few points in UMD.
OTHER CONSIDERATIONS
Since so much of the rogue I'm describing here is invested in sneak attack it could really suck when you face undead and constructs, right? Not necessarily. There are a couple of alternate class features which mitigate this weakness- Penetrating Strike (Dungeonscape) and Death's Ruin (Complete Champion). Both of these replace the trap sense class feature for rogues so keep that in mind if that bonus vs. traps is important to you. Penetrating Strike gives you half your sneak attack damage against things normally immune to sneak attacks, but only with flanking attacks. So you still can't sneak attack things which are immune and can't be flanked, such as oozes and elementals. But it covers the big rogue-banes: undead and constructs. If your mainly concerned with undead then go with Death's Ruin. It allows both flanking and flat-footed sneak attacks, again at half damage, but only against undead. It's also a supernatural ability so it won't work in anti-magic fields- if that's a concern.
Wow, it looks like I've gone on a lot longer than I intended. I could go on but I think I'll stop now. Hopefully some of this advice is useful.
