There are very few GBA programs that can talk to your card's filesystem. Much more common are GBA programs with built-in filesystems. In addition to the goomba.gba emulator core, you will need the Goomba frontend to add games to it to produce a single large *.gba file containing all of your games. This will need to be 32 MB in size or less to run from NOR or 16 MB or less to run from the 3in1's RAM.
Instructions:
1. Grab the Alpha 6 package from
http://www.pocketheaven.com/boards/viewtopic.php?t=3280 which includes the emulator core and builder application
2. Grab the updated goomba.gba emulator core from
http://www.dwedit.org/dwedit_board/viewtopic.php?id=229 and use it to overwrite the old one in the previously downloaded folder.
3. Follow the instructions at
http://wiki.pocketheaven.com/Goomba to create your compilation. Do not save it as "goomba.gba" or you'll overwrite the emulator core. Save it as something different like "GBCgames.gba" or something like that
4. Copy it to your microSD card and launch it like a regular GBA game.
EDIT: as for the original question, I've heard that PCE emulation is really only available on the GBA, while SMS emulation is a tossup between the DS and GBA emulators.
PocketNES has received some fixes for specific games that NES DS has not been updated to include.
Herg's Solitaire is an amazing compilation of many different card games and is only available on the GBA. I'm not sure if anything of the same caliber exists for the DS, but I haven't really looked into it. Perhaps Puzzle Maniak includes games like that.
SNEmulDS should be able to utilize the 3in1's RAM, so see if that helps playability at all.