[Kirby]

from the VisualBoyAdvance page:

SDL stands for Simple DirectMedia Layer. It is a cross platform library for graphics, input, audio, threading, etc... that can be used for games, emulators, etc.
VisualBoyAdvance has a special version that uses the SDL library and that provides the same behaviour on the different systems it as been ported to.

To some people, the SDL version on Windows may be faster than the DirectX version.

The main difference with the Windows version is that it is command line driven, meaning you have to type arguments at the command line in order to run. Configuration is archieved by editing a text file.

Another big difference is that the SDL version has built-in debugging features (ARM/THUMB debugger, multiple breakpoints, RAM write breakpoints, etc...)

More debugging features will be available on upcoming versions.