VirtualBox allows you to run a whole OS (probably XP) within the program. It acts as the hardware for the guest OS, allows you to choose RAM, HD etc. WINE on the other hand, acts as the OS for Windows programs, and allows you to choose 98, 2000, XP.
If a program is just making calls to functions that Windows normally provides, then WINE will basically point it towards the Linux version of those functions (SCAR). If the program needs Java (RS), you need to install the Windows version of Java in WINE. If the program needs the .NET framework, it probably won't work with WINE (Mono might work, but that's another story). If it needs both (Scion), or uses something that WINE can't translate (see
here for how well WINE works with popular apps) then you will need to install a full blown XP within VirtualBox.
Whenever you think of something you need, just google 'ubuntu _______ alternative', most of the time you get something equal or better, and won't have to worry about WINE and VirtualBox.