I noticed that the extracts are used like potions. Does this mean he has to use a move action to ready the extract from his belt/backpack etc. and then a standard action to drink it? This seems awfully harsh. I think he should have an ability akin to quick draw but usable with any items including potions and scrolls. This could replace the Throw anything feat, which I really don't understand why he gets at all.
Another thing I would like to have seen was an ability to mix extracts to get the benefits of multiple extracts at the same time. Say at 10th level or so he gets the ability to combine to extracts but of no higher level total than the highest level of extract he can prepare f.ex. this could increase to three effect at 20th level. There could be a fun side effect table for mixing extracts to add some risks to the process. Also the ability to add metamagic effects to his extracts.
When it comes to bombs I would like to see a class feature or discovery which allowed him to throw multiple bombs in one round.
I would also like the alchemist to be able to prepare all spells that affect a creature as extracts, but he has to learn it just like a wizard learns spells and put it in a book of recipes. I really hate classes with new spell lists, it makes it so hard to implement material from other sources like the spell compendium, and if it is one class that should have a large list of spells it should be the alchemist. This would be very easy with this class just list a number of schools and sub-schools appropriate for the alchemist and a note that only effects that affect a creature can be learned. Have him progress much like a wizard and with no limit to how many recipes he can learn, but he has to add them to his recipe book at the same cost it takes for a wizard to add spells to his spellbook.
Not to sure about the poison use aspect of the class, I think this should be a discovery so that those who wanted to explore such avenues could, but it wouldn't be an essential class ability.