I don't have time at the moment to go through that awesome list, so apologies if any of these are repeats.

BAMF!Tony
Hostile Takeovers (http://truthiness-aura.livejournal.com/28650.html) by truthiness_aura
The Linchpin (http://archiveofourown.org/works/468810) by canarynoir
Space Electric (http://archiveofourown.org/series/26507) series by icarus_chained
Truths, Lies and the Tipping Point (http://archiveofourown.org/works/381279) by BlackEyedGirl
More Worthy Than Believe (http://archiveofourown.org/works/606692) by LadyShadowphyre
Tony and Bruce series (http://archiveofourown.org/series/17981) by icarus_chained

not-quite-human!Tony
Blue As True As Blue Can Be (http://archiveofourown.org/works/648087?view_full_work=true) by aaralyn (mutant!Tony)
Leopard Spots (http://www.fanfiction.net/s/8337900/1/Leopard-Spots) by SlateWalker (wereleopard!Tony)
What Lies Inside (http://talesofsuspense.net/viewstory.php?sid=293&chapter=1) by Penumbren (werewolf!Tony)
Turn Around (Three Times Before Lying Down) (http://archiveofourown.org/works/401627) by kellifer_fic (werewolf)
Got the Cream (http://archiveofourown.org/works/341817?view_full_work=true) by TARDIScrash (cat-to-human!Tony)
Catechism (http://archiveofourown.org/works/507496?view_full_work=true) by manic_intent (angel!Tony)
House of Odin (http://archiveofourown.org/series/14407) series by MoiraiThanatoio (Asguardian!Tony)
Waking the Dragon (http://archiveofourown.org/works/383159/chapters/626849) by tsukinofaerii (dragon!Tony)
Turning Over a New Claw (http://archiveofourown.org/works/548230?view_full_work=true) by AnonEhouse (dragon)
Dreaming Electric (http://archiveofourown.org/works/547577) by jukeboxhound (MCU!Extremis!Tony, written pre-IM3 no spoilers)
There is no I... (http://archiveofourown.org/works/128951) by jadedoll (cyborg!Tony)
Find a Way (http://archiveofourown.org/series/38859) series by Gir_Hugs (hacker!Tony)
festina lente (hurry slowly) (http://archiveofourown.org/works/505333) by silverfoxflower (Captain America!Tony)