Universal Remotes:

HippoRemote Pro

Easily one of the sleekest designs in the UR category, the HippoRemote app provides an excellent way to control your home theater PC or media center.  It provides a trackpad, keyboard and plugins for a variety of platforms including Boxee and Twitter.  It’s also compatible with Macs, PC and Linux systems.  The multi- functionality replaces the standard Apple controls for good and is easy enough for anyone to use.  Link ($4.99)   

Note: There’s also a free version and a Lite version ($2.99), if you want to try it first.)

Flpr

If you are interested in turning your iPhone into an IR device, New Potato Tech sells a $79.99 device that pops onto the top of the iPhone / iPod Touch and turns it into a universal remote.  With the application, you can add devices by brand and control your home theater components with a couple simple taps on the iPhone.  Link  (Free)

iMastercontrol Pro

This application is not targeted at the typical home theater consumer, but rather it’s designed for home theater gurus that use either a Crestron or AMX system to control their home theater and/or lighting.  It’s ideal for installers setting up these new systems in homes or for the savvy consumer that wants to try their hand at programming the system themselves.  Link ($149.99)