You beat me to it! I wanted to be sure that anyone reading this thread saw that the original suggestion of ModernBill was from in 2006 (when the software was one of the best on the market). The thread was rehashed again in 2008 and now here again in 2009.
I've used many various types over the years, even purchased ModernBill when it was $49!!! Now who else can remember that far back with the budding software? I had the pleasure of meeting Michael Fountain a few times over the years and we even did a bitch session about just what was wrong in version 4 and how awful the version 5 prototype was looking. I'm happy that they finally saw when to get out of the market and let someone else take over.
I've used Ubersmith, but due to the number of servers and the monitoring needed, we needed the DE version which was very expensive for what it did.
In late 2007 we moved to WHMCS and really haven't looked back. We've developed a few different tools for integration to get the software to do more things than it was designed to do, and for an "Out of the Box" solution it's a tough one to beat! Support is also good, and the community is fairly quick to post help when they can.
The downside to using an inhouse product is the certification and requirements that will be needed to pass PCI Compliance. The up side is that you know EVERYTHING that's in the software and it does exactly what you want to do. If you have the money, custom is usually a good solution.
As for DHD-Nick, what would you like to see different in WHMCS or CE? Personally I think the billing market is pretty covered at this time, but a server monitoring program, server inventory control and software version tracking information is software that is actively being seeked by various places. Would love to head up that project, but I'm not in a position to invest the money needed currently