It's hard to swing a dead cat without hitting someone selling one kind of remote control, or another. Because of their lack of communication and dealer support, I can't recommend Harmony. I was a dealer until I made the decision Friday to never sell another one. They don't make replacement batteries available to their dealers or distributors, which makes it hard to care for customers whose remote fails on a weekend and calling the dealer support number was basically a waste of time. Radio Shack and Best buy sell them but they can't get batteries, either. I had to settle on a replacement that fits but the reserve capacity is about 15% less, which means she'll have to recharge it more often which usually means that it'll start acting up while it's being used.
URC makes a wide variety of remotes- some are only IR and some do IR and RF.
DO NOT buy the cheapest one you can find. If you want to hate life itself, that's a good way to get there. How a remote is programmed makes a big difference in how well the system operates. You can use an IR repeater but they don't work well in rooms with plasma TVs, lots of sunlight and compact florescent lights.
In order to really make a recommendation, you'll need to list your equipment and define how much control you want. FYI- if you want to dim your lights, URC has models that use Z-Wave, which will operate Leviton, Lutron and Intermatic dimmers. IR controlled dimmers are available, too. If you use the Z-Wave type and an RF remote, you can include light dimming into your macros, which is pretty useful. Also, if your system has a lot of different pieces, anything from the URC MX-650 will control about 15 devices.