Places to check for Alchemy stuff;
PHB 3.5 (p 70-71, 128-129)
Acid
Alchemist's Fire
Antitoxin
Smokestick
Sunrod
Tanglefoot Bag
Thunderstone
Tindertwig
Book of Vile Darkness (p 41-44
Feather Powder
Festering Bomb
Weeping Stone
Agony (Liquid Pain)
Baccaran
Devilweed
Luhix
Mordayne Vapore (Dreammist)
Mushroom Powder
Redflower Leaves
Sannish
Terran Brandy
Vodare
Libris Mortis (p 73-74)
Brittlebone
Embalming Fire
Ghostoil
Liquid Night
Races of the Dragon (p 122-123)
Bitterleaf Oil (DC 15)
Ditherbomb (strong (DC 20), weak (DC 15) or wyrm (DC 25), can’t take 10 on these checks)
Fire Beetle Lamp (DC 10)
Sundark Goggles (DC 15)
Races of the Wild (p 168)
Leafweave Armor (also requires Craft (armorsmithing))
Races of Stone (p 159-161)
Blasting Pellets
Blister Oil
Hearthfire
Spiderlily Essence
Complete Mage (p 134-135)
Auran Mask
Crackle Powder
Fast Torch
Screaming Flask
Weeping Flask
Complete Adventurer (p 118-122)
Blend Cream
Focusing Candle
Catstink
Fareye Oil
Flash Pellet
Freeglide
Hawk's Ointment
Healer's Balm
Keenear Powder
Lockslip Grease
Nature's Draught
Softfoot
Suregrip
Antitoxin Capsule
Ironman Capsule
Leap Capsule
Stability Capsule
Strongarm Capsule
Swiftstride Capsule
Ghostblight
Quickflame
Quickfrost
Quickspark
Quicksilver
Draconomicon (p 116-117) *requires Dragoncrafter feat*
Blood Elixir
Lords of Madness (p 114-115) *requires Grell Alchemy feat*
Grell Crystal
Lightning Lance (magic item, requires Alchemy)
Greater Lightning Lance (magic item, requires Alchemy)
Silver Spear (magic item, requires Alchemy)
Heroes of Battle (p 134-137)
Acid Stone
Alchemist's Stone
Holy/Unholy Stone? (should require a priest, not an alchemist)
Tanglefoot Shot
Stormwrack (p 108)
Stinkpot
Frostburn (p 78-79)
Armor Insulation
Freeze Powder
Frostbite Salve
Ice Chalk
Melt Powder
Polar Skin
Razor Ice Powder
Whale Grease
Sandstorm (p 101-103)
Armorbright
Blackeye
Deep Draught
Ironthorn Extract
Keepcool Salve
Shapesand
Slumber Sand
Sunshade Lotion
Special: Oleum (no Alchemy Craft DC, but it seems like it should be craftable)
Arms & Equipment Guide (p 32-35) *some repeated in Cadv*
Bladefire
Acid Bullet
Flame Bullet
Focusing Candle
Restful Candle
Clearbreath
Darkvision Powder
Defoliator
Dehydrated Food
Dwarfblind
Farflame Oil
Fleetfoot
Ghostoil
Gravebane
Hawk’s Ointment
Instant Rope
Longbreath
Motelight
Nature’s Draught
Polar Skin
Signal Torch
Sparkstone
Stonebreaker Acid
Verminbane
Vicious Bleeder
Savage Species (p 46-48)
Breathing Mask
Flashtube
Frostfire
Sculpter’s Slime
Eberron Campaign Setting (p 120-121)
Acidic Fire
Alchemist’s Frost
Alchemist’s Spark
Noxious Smokestick
Magic of Eberron (p 139-140) *no Alchemy Craft DCs*
Bloodspike (defiling)
Bloodspike (glowbug)
Bloodspike (spatter)
Bloodspike (tempo)
Bloodspike (thickener)
Faiths of Eberron (p 153-154) *no Alchemy Craft DCs*
Breath of the Devourer
Euphoric Sacrament
Flayskin
Mordrei’in
Silverburn
Oriental Adventures (p 78)
Eggshell Grenades (dust, flashpowder, pepper, poison smoke)
Flash Paper (moeragara)
Jade Powder
Liquid Smoke (ekitai kemuri)
Sleeping Fire (hinemuri)
Forgotten Realms Campaign Setting (p 96-97)
Alchemical Sleep Gas
Disappearing Ink
Scentbreaker
Dungeonscape (p 34-37)
Acid Neutralizer
Bottled Air
Firmament Stone
Ghostwall Shellac
Lava Stones
Lockslip
Trollbane
Drow of the Underdark (p 93-94)
Bile Droppings
Darkvision Powder
Dwarfblind Stone
Shedden
Spelunker's Oil
Stoneburn Acid
Vilegrip
Dragon magazine 280, article Better Living Through Alchemy, has some great stuff. Issue 301 also has a large article on Alchemy, but I don't recall it specifically. Quite a few (perhaps even all of them) seem to be reprinted in the Dragon Compendium.
Places checked;
PHB 3.5 (p 70-71, 128-129)
Book of Vile Darkness (p 41)
Libris Mortis (p 73-74)
Races of the Dragon (p 122-123)
Complete Mage (p 134-135)
Complete Adventurer (p 118-122) quite a lot of ‘em
Draconomicon (p 116-117) requires Dragoncrafter feat (only 1 item)
Lords of Madness (p 114-115) requires Grell Alchemy feat (only 3 items)
Heroes of Battle (p 134-137) alchemical siege shot
Stormwrack (p 108)
Frostburn (p 78-79)
Sandstorm (p 101-103)
Arms & Equipment Guide (p 32-35) quite a few, some repeated in CA
Savage Species (p 46-48)
Faiths of Eberron (p 153-154)
Eberron Campaign Setting (p 120-121)
Magic of Eberron (p 139-140)
Oriental Adventures (p 78)
Forgotten Realms Campaign Setting (p 96-97)
Drow of the Underdark (p 93-94)
Of 3rd party stuff, the best one I’ve seen for a meaty and balanced selection is the Kingdoms of Kalamar Players Guide (p 113-116), but you can also find a few gems in other Kalamar products, in Monte's Arcana Unearthed, in Relics & Rituals 2, etc, etc. if you have them lying around.