Does the Bose system just respond to RF signals (as opposed to infrared)? If so, you won't be able to control this with a universal remote.
Moving on, the next question is, do you want a touchscreen or a buttoned remote?
If you want a touchscreen, there are many choices, there's the Pronto, the Sony AV2100, the uCommands, etc The top of the pile is definitely the Pronto as it's totally customizable and you can program it from your PC.
In between, there's the MX500, which has quite a few buttons and a small LCD screen for the more unusual buttons.
If you really want a buttoned remote, I would recommend any of the higher end One For All or Radio Shack remotes, as these allow you to re-program individual buttons using "advanced codes".
If you really want to get advanced, you can re-program OFA and RS remotes using JP1 from your computer.
Rob.
http://www.hifi-remote.com