There a
lot of choices available in aftermarket remote controls, ranging from simple $15 "universal" remotes to $1000+ uber-remotes and everything in between.
If you haven't done so I would suggest visiting
RemoteCentral. It is one of the best sites available on the subject of remote controls. There is a section with reviews of quite a few remotes. There are articles on the subject, the "Clicker Picker", and of course the forums.
Your remote control is your primary interface with your television/home theater setup. If you had spent, for example, $500 on your setup it would
not make sense to purchase a remote costing much more than $40-$50.
If, however your system consists of multiple devices (HDTV, HD sat receiver, sat dvr, dvd player, cd player, HT receiver) costing several thousand dollars it's a lot easier to justify the cost of more expensive remote. Especially if the remote is capable of supporting macros to automate complex power/input sequences. Press one button and the TV turns on, HT receiver turns on, satellite receiver turns on, TV switches to satellite receiver input and HT receiver switches to satellite receiver input.