Ian K., Roll20 strives to be as system agnostic as possible. We've had people play everything from Settlers of Catan to Savage Worlds and more. My own experience has found Roll20 to be pretty flexible. If you haven't had the chance yet, check out the Roll20 Wiki for more information on all the different things that are available to you. If you have questions about how to do something specific for your custom RPG, just post in the Specific Use Questions Forum and I'm sure you'll get plenty of help figuring out a way to make it work. Don't be shy about asking questions of any sort. I think you'll find the community here to be pretty awesome. Welcome aboard! :)
