I can't believe in the time I've been here I have completely overlooked this emulator.
Here's my problem: I don't know how to use the EXE. I tried double clicking it, like I would some EXEs, and the window flashes on the screen before quickly disappearing. So I tried dragging the SMS and GG ROMs individually into the EXE. Same thing happens. A flash of a command window and then it's gone with no NDS or GBA file given. I even tried creating a folder and putting everything in the same folder (like I've done with NDStool) in hopes of getting anything. Nope. Same thing.
What am I doing wrong?
I used the DSMS download available on this site.