I try to break up the options into the technology:

Cases
Surc iPhone 4/4S Case
Zero1 Voomote Zapper
Power A for iPhone 3G/3Gs

IR Dongles
Think Flood RedEye Mini
New Kinetix Re (iPad optimized App)
New Potato FLPR
I Got Control IRB1 (closeout)
L5
iWavIt
Zero1 Voomote 1

Bluetooth
Griffin Beacon Dijit (separate versions for iOs or Android)
MiCommand Control It All
MiCommand Control It All with AirDoc (wireless bluetooth audio streaming)
Gear 4 UnityRemote
Acoustic Research Zentral (killed almost immediately in US)

Wifi
Logitech Harmony Link (iOS, Android)
ThinkFlood RedEye Wifi Gen 1 (iOs, Android, PC or Mac)
ThinkFlood RedEye Wifi Gen 2 (adds IR out jack) (iOs, Android, PC or Mac)
ThinkFlood RedEye Pro (iOs, Android, PC or Mac, adds RS232 & routable IR)
SquareConnect SQ Blaster (with zwave) (iOs, Android with TotalControl Remote Edition, PC or Mac)
Peel Fruit

Software Only requires Global Cache or other Hardware
Bitwise Controls
iRule HD
Demopad
Total Control Remote Edition (Android)
TouchControl
Command Fusion
RoomieRemote

Hardware used by the Apps
Global Cache
Square Connect SQ Blaster
irTrans

Don't forget that most traditional control vendors have complimentary apps as well including:
Crestron
RTI
URC
Control 4

Apologies if I missed any.