If you have something that you feel is truly innovative, then patent it! Software patents can be abused by trolls, but if you are worried they will patent it in the future and make your life miserable, your best bet is to patent it now, before they do.
I guess your other option is to open-source it, though I'm not an expert and I don't know if that would make it impossible for others to patent in the future - and that might not be compatible with your business model.
Oh yeah, and you might want to talk to a patent lawyer as well, because they will probably know more than I do about this sort of thing. ;)