With the new 3rd edition, and the Open Gaming Lisence, you can in fact use the 'd20 system' in your own products. The whole system (in it's vanilla-non-T$R format) is maintained at:
http://www.opengamingfoundation.org/srd.html
If you use only the content that has been approved and abide by their rules, you can legally do it. And it has specifically been addressed whether it makes a difference that it is on paper or on the PC - it doesn't. Just so long as the code containing the game mechanics meets the rules. It's all on WoTC's site too.