As Gigi said, you need to reinstall from scratch. There is too much changes between 2003 and 5.0, and only sprite backup 5 works with WM5 btw. Also, don't worry about the VGA compatible software. Most QVGA applications have no problems running on a vga device. VGA optimized softwares just appear nicer. What you really worry about, as you stated in your post, is WM5 compatibility. Check out this site:
http://www.wm5fixsite.com/ FYI, most commercial software developers have already updated their software to support the new OS.
If you can post the list of program you want, people here might be able to tell you whether they're compatible with WM5.