The old Arms and Equipment Guide has some nice alchemical items in it.
One simple solution is to create variants of existing alchemical items.
Instead of Alchemists fire, you could have alchemist's Frost (cold), Acid, and a suped-up thunderstone that instead of being a glorified flash-bang, simply does sonic damage.
mage. Simply pick an energy type and have it only do 1d4 damage. Take the DC for Alchemical fire and let the GM add +1 or +2 to the DC for non-fire based items as he sees fit.
Although the Brew Potions feat makes sense for 1st level and higher spells, most alchemical items I have see that cause damage are basically the equivalent of 0-level spells; 1d3 or 1d4 damage.
Ask your GM if he would allow you to use craft-alchemy to make one-shot 0-level potions. I've allowed this as a GM and it isn't so powerful as to cause problems. So you could make an ointment that when applied to an object would glow if it's magic, mimmicking Detect Magic.
Or a potion that grants a +1 bonus to save for a few rounds like the Resistance spell, or a alchemical coating that duplicates the light spell.
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...you know the rest, I recently compiled a 16-page document of all the alchemical stuff I could find in my sizeable 3.5 collection. It's all from WotC books, so shouldn't raise as much concern as some of the wonkier third-party stuff. (And don't get me wrong, some of the third-party stuff seems to be more reasonably developed and tested, but still.)
One item in particular gives penalty to Fort saves, awesome for a poisoner. (I was looking at this one for an Alchemist/Fighter I was going to play, coating spiked gauntlets, armor spikes, and shield spikes with poison.) There's tons of other stuff that creative characters can have fun with, too.