Since I've bought every Humble Bundle (excluding some weeklys), I figured I'd go through all the available Android games from them and check their compatibility with the OUYA.
A quick note about the Humble Bundle app, for whatever reason, I've found that every time you exit and reenter it, you must log out and log back in to access your Humble Library.So here is the list of all the games I tried (installed using the Humble Bundle App) and the results... Games listed as being playable with the touchpad would obviously work better using a mouse, but based on my opinion, I felt they were at least functional with the touchpad.
Runs and works with Controller(s)Another World (Tapping Middle Button brings menu up, but then quickly goes to title)
Canabalt (Humble v1.1, OUYA v2.02)
Dynamite Jack (Need to manually set button controls)
EDGE - Classic
EDGE - Extended
Metal Slug 3 (Not playable with Xbox 360 Controller)
(Unable to Use Credits/Continue After Death)Raiden Legacy (Not playable with Xbox 360 Controller)
Solar 2
Super Hexagon
Runs and Playable with TouchpadAquaria [ADDED 06/18/2013]Anomaly Korea
Anomaly Warzone: Mobile Campaign
Broken Sword: Director's Cut [ADDED 06/18/2013]Cogs
Contre Jour
Fieldrunners
Frozen Synapse (beta) (Unable to zoom) [ADDED 06/18/2013]Machinarium (Mobile (>1024x600)) (must make fast touch movements for such a large play area)
McPixel [ADDED 06/26/2013]Osmos (Mobile)
Plants vs. Zombies
Sleepwalker's Journey [ADDED 06/18/2013]Spirits
Splice
Superbrothers: Sword & Sworcery EP
Swords & Soldiers HD
Waking Mars
World Of Goo
Zen Bound 2
Avadon: The Black Fortress (Tablet)*
Machinarium (Tablet (>1280x800))*
Osmos (Tablet (>8"))*
SpaceChem (Tablet (>5"))*
Uplink (Tablet (> 7"))*
Runs, but very difficult or impossible to play with TouchpadBIT.TRIP BEAT (Possibly Playable with Mouse)
Beat Hazard Ultra (Possibly Playable with Mouse)
Crayon Physics Deluxe (Possibly Playable with Mouse)
Dungeon Defenders + All DLC
Eufloria HD (Possibly Playable with Mouse)
Fractal [ADDED 06/18/2013]Funky Smugglers (Possibly Playable with Mouse)
NightSky (Possibly Playable with Mouse)
Organ Trail (Humble v1.6.6.3, OUYA v1.6) [ADDED 06/18/2013]
Pulse [ADDED 06/18/2013]
Serious Sam Kamikaze Attack
Smuggle Truck
Snuggle Truck
Stealth Bastard Deluxe (Works with OUYA controller, for Left/Right/Down...but no jump; does not work with 360) [ADDED 06/18/2013]The Room
Unable to StartBladeslinger (Loops while loading)
Toki Tori (Kicks back to home screen)
*Listed by Humble Bundle App as Unsupported
Sorry if this list is a bit strange to some, I just felt it was the best way to display the information for any person regardless of technical expertise...and if I missed any Humble Bundle games, let me know or post your own results and I'll add them to the list.
And for reference, here is the information from the Humble Bundle App. Additionally, these were all tested on the OUYA 1.0.5 firmware.
Device Model OUYA Console
Humble App Version 1.3.3
OS Version 4.1.2
Screen Layout large
Screen Width 1920
Screen Height 1080
I've also gone ahead and posted this list at the following locations...
CAGXDA 
EarthBoundX5
Posts: 9Member
Comments
EDIT: Bundle bought, installing and testing everything now...might take a bit since 3 of the games in the bundle are ~500MB
EDIT 2: Bad news so far...
EDIT: Currently in process of testing Mobile Bundle 2, will purchase and test Android 7 after...
EDIT 2: Done with MB2, bought Android 7 and beginning testing...
EDIT 3: For whatever reason, I cannot edit the OP (the option is not even shown)...so I will post my added findings as a reply... I suggest in the future to follow my other posted threads on CAG or XDA...however, I will continue to also add updates here, just not in the OP...
Runs and works with Controller(s)
Anodyne (Continue and Back Button are Mapped to same button...could be problematic...) [ADDED 10/20/2013]
Incredipede [ADDED 10/20/2013]
The Bard's Tale [ADDED 10/20/2013]
Time Surfer (EVEN SHOWS UP IN PLAY SECTION) [ADDED 10/20/2013]
Runs and Playable with Touchpad
Greed Corp [ADDED 10/20/2013]
Ticket to Ride [ADDED 10/20/2013]
Runs, but very difficult or impossible to play with Touchpad
Bloons TD 5 (Possibly Playable with Mouse) [ADDED 10/20/2013]
Carmageddon [ADDED 10/20/2013]
Karateka Classic [ADDED 10/20/2013]
Punch Quest [ADDED 10/20/2013]
QWOP [ADDED 10/20/2013]
Star Command (Possibly Playable with Mouse) [ADDED 10/20/2013]
Worms 2: Armageddon [ADDED 10/20/2013]
Unable to Start
God of Blades (Does not take touchpad as tap to start) [ADDED 10/20/2013]
Ravensword: Shadowlands (Cannot select anything when prompted to use detected controller...) [ADDED 10/20/2013]