I recently acquired a FLIRC USB Dongle
FLIRC is a USB programmable adapter that can learn from any IR remote controller. You program the FLIRC using an app running on a Mac, PC or Intel based Ubuntu install, and once setup the FLIRC just appears as a standard USB keyboard.
The FLIRC itself is the size of a small USB stick – I’ve been using it with an old SKY box remote which has lots of handy buttons to use for various options. These remotes are a nice size, take AA batteries, and there are plenty available from amazon 
Each of the keys is set by running the FLIRC app – this can be set up as a simple apple TV remote:
for a more complicated XBMC remote, compatible with the Raspberry Pi’s RaspBMC:
Or for the full kitchen sink option, as a complete USB keyboard:
The latter is particularly useful as it offers keys like left and right command – which are missed off some keyboards, like the one on the Motorola Lapdock and using a small remote as a keypad is also quite a handy feature. Programmable keypads are usually much more expensive than the £22.99 that the FLIRC retails for.
All in all the FLIRC is a handy tool for the Raspberry Pi – it’s only downside is that it can’t be programmed directly from the Pi itself, as you need an intel based Mac or PC to program it. There is an API promised in the near future that should hopefully address some of these issues.
One possible option would be to use the Pi as a bluetooth adapter, thus allowing you to control your iPad with an ancient Sky remote.