http://www.tvsian.com/

I found this a few months ago, played it a bit then lost it when I formatted. It allows you to create teams, with movesets from Red/Blue/Yellow/Green/Gold/Silver/Crystal. The creator is planning a huge update in a few months that will include Ruby/Sapphire as well as a better way of setting up teams and saving them.

http://www.tvsian.com/netbattle/downloads/NBFull.exe

The link to the full download. The program allows you to make teams of 1-6 Pokemon with moves they can learn. You can host your own server or join the main server and battle against other players.