There are plenty of solutions to your situations, and you've come to the right place to find answers.
The Pronto can handle just about everything that you can throw at it and it's programmable from your PC, but it is expensive and it is a touchscreen. Some people love touchscreens, some don't.
Then there's the MX-500 which costs around $100. It's got tons of learning memory, so you'll have no problems learning all your stuff, plus it's a buttoned remote with an LCD screen that you can customise for some of the more unusual buttons.
Finally, there's One For All remotes with JP1. This is definitely the option to follow if you're on a budget, but for some of us, this is the perfect solution regardless of budget. JP1 is a home made process that let's you hook your remote up to your computer and re-program it. If your One For All remote is a learning remote, you can use this feature to capture the signals and build upgrades. The learning URC-8811 remote can be had for $19 and a JP1 cable runs about $15.
Rob
http://www.hifi-remote.com