Crestron/AMX - These control system based units not only will control all your IR devices, but will integrate with any RS-232 controllable devices (ie: Yamaha & other higher end receivers) very well. Some remotes are hard wired, but many use RF for wireless communication (not IR). This means that your equipment can truly be buried with no IR repeater system or anything else. AMX does have some with IR capability.
A Crestron, entry level package with a RF receiver, control system, and 5.7" color touchpanel is (MSRP) $3,800.00 (plus you will need programming)
Less expensive is the system with a hard button remote that has the same processor & RF receiver for $2,150.00
What is the beauty of these systems? Well, the main thing is that the theater is just the beginning - they are very, VERY expandable. If you aren't happy with your current remote, then get a new one, a bigger one, a smaller one, whatever. It will work with the control system you have. You can use 20+ remotes, or just one remote with the system. You can actually utilize zone 2 (or 3) of your system to pump audio around the house and have a remote that will control it from anywhere in the house. Tested range on the RF is about 1,000 feet... how big is your house?
I use Crestron myself and really like the ML-500 which is their hard-button remote. The control system ensures that all commands are properly performed and I can switch between my plasma display and my projector with the touch of a button. All sources are one-touch available, and there is tons of practical functionality available to me. I also have an older touchpanel & web control. The web control uses Internet Explorer so I can monitor and check my system from anywhere in the world.
Anyways: The option is the Pronto and Marantz style remotes which basically use IR and do not have a lot of additional logic available to them to control systems. You can learn any IR remote with them and they are in the $300-$1,000.00 range. They will also need to be programmed. I have heard (and seen) very mixed results with the RF adapters available for them. They also can be a little picky about learning some codes. Finally, I have heard of basic problems with their memory being lost sometimes. But, they do a far superior job than many other remotes on the market and offer a touchpanel for style, and macros to automate startup and shutdown procedures.
Check
www.ebay.com for used Crestron & AMX gear and you will always find some very good prices that may run half of MSRP - or less. Also, Yahoo user groups have a great Crestron forum.