For me I just use one remote.
http://www.ofausa.com/remote.php?type=URC%209960
I have the following setup to work with it:
1.) Toshiba 27" TV
2.) Aiwa Stereo (Really Old)
3.) Harman Kardon DVD Player
4.) DirecTV Receiver
Also, if I have any kind of special functions that I want to use the remote for, I can easily reprogram the remote either using learning on the remote or through a PC.