Inferno Bomb - This is actually pretty solid with the FAQ explanation that the Inferno Bomb damage is
in addition to your regular bomb damage, effectively giving an additional 6d6 damage to your bomb (in addition to the battlefield control/vision hampering effects)
Infuse Mutagen - Not really seeing a purpose to this, possibly red.
Infusion - Allows your party to use your infusions. I could possibly see downgrading it to blue, but I feel this is a no-brainer if you have a discovery open (or as a first discovery gained).
Lingering Plague - Disease isn't that great to begin with. Possibly red.
Lingering Spirit - Situational, but possibly useful.
Madness Bomb - No-save Wisdom damage is fun, but it's hard to rack it up. Still potentially debilitating to a cleric or druid, and it can soften someone up for an important Will save effect from a party member.
Malignant Poison - Wow. This is great for poison users. Too bad by level 10 they're already long overdue for something like this. Could be much better if your DM lets you take it early.
Mummification - Immunity to cold, nonlethal damage, paralysis, and sleep for a discovery is wonderful. Needing to wait a month is not.
Talk to your DM to see if mummification is right for you.
Mutagen - If you need it, you already have it from taking a level of alchemist. If you dropped it for an archetype, you probably don't need it.
Nauseating Flesh - Cute. Could go green to red depending on the prevalence of creatures with bite attacks in your campaign.
Parasitic Twin - If only it wasn't once per day. Still, it kicks in once you've already failed the save.
Plague Bomb - Potentially red. Diseases have pitifully low DCs.
Greater Plague Bomb - Potentially red. I feel like there's some use if you can soften up an enemy, but this really only feels like its good for a plot device ("Oh, no! The village is diseased!")
Poison Bomb - Cloudkill + bomb damage? Only one level after the Wizard gets it? Pretty sweet.
Poison Conversion - Oh, poison. Poison, poison, poison.
Precise Bombs - This is pretty important unless your allies all have immunity/heavy resistances to your primary bomb energy type. Obviously worthless for non-bomb users.
Preserve Organs - It's probably better to just shell out the gold for light fortification armor, but you can get it from level 2, and critical hits are a leading cause of death in low level characters.
Rag Doll Mutagen - The bonus on Escape Artist is a poor man's freedom of movement. But you get freedom of movement from the alchemist extract list, so this is just a poor choice.
Ranged Baptism - Hilariously named, but impractical.
Rocket Bomb - More chances to hurt your allies? Can't be used with two of the leading discoveries? Hooray!
Scrap Bomb - Its one saving grace is that it doesn't have an asterisk, meaning it can be stacked onto any bomb. By RAW, it looks like it can be mixed with Breath Weapon Bomb, allowing you to cough shrapnel onto your foes.
Shock Bomb - Electricity is less likely to be resisted than fire, but dazzled is just worthless. Go with Acid Bombs or Frost Bombs if you want to shift elements without DPS loss.
Siege Bomb - I don't know enough about the siege weapon system to accurately rate it.
Smoke Bomb - Possible blue. Stack battlefield control onto your primary damage ability.
Spontaneous Healing - The one thing I really have to recommend it is the fact that it's a free action, but this is potentially red.
Healing Touch - The only reason I can see to taking it is increasing the amount of healing from Spontaneous Healing each day.
Sticky Bomb - It's a straight DPS increase that stacks with everything (it's essentially adding Int+number of bomb dice to every hit). It applies on direct hits, so sticky breath away!
Sticky Poison - I feel like there's a sweet spot for a poison alchemist right about level 6. This is solid for them, plus they get swift-action poisons at this level.
Stink Bomb - Nausea+battlefield control+damage all in one go? Heck, yes!
Strafe Bomb - Interesting but mostly impractical. Feels like it would be really good in cramped hallways or as an alternative to Precise bombs.
Sunlight Bomb - +2 damage per die to undead is potentially useful, as they're one of the most common enemy types.
Tanglefoot Bomb - Not bad. Sadly has an asterisk and can't be combined with other kinds of bombs.
Tentacle - It's fancy, but possibly red.
Tumor Familiar - Familiars are already a good value as an extra set of actions each round, plus a skill bonus (or initiative bonus!), plus alertness, plus the disgusting mental image. Possibly blue. Also, check out
Die for Your Master.
Underwater Demolition - This is pretty awful. Even if you're going underwater, this is pretty awful.
Vestigial Arm - I've seen some creative things done with this and Gunslinging builds. Probably red for general use.
Wings - Extraordinary flying. 'nuff said.