I use freeSide; not sure I'd recommend it, but hey, open source and it handles things like service credits much better than most of the webapps I've tried. I use paypal and/or checks for actual billing

I'm considering switching to one of the webapps you kids seem to like, but most of them seem more like payment processors than billing systems, really, and if I have to maintain my own separate billing system, what's the point?

I am very interested in what other people's experiences have been with the webapps, though.