I haven't tried many, but NesDS works pretty well. Sometimes it dosent show all the levels of graphics in the right order or some of the sound effects are missing.
SCminiSD here.
SNES compatibility bugs me as well. You can run the GBA remakes of SNES games, but they slow down like crazy and eat batteries Very fast. - I wish I had spent the extra cash for the M3.
I can get SnesDS to load up games but when the actual gameplay starts, it freezes. Also, my SC won't let me use it's commands to go to the menu, save real time, et all.
ADDED:
here's how to use NesDS:
1. run the unzipped nesDS.exe and click save - don't add any games
2. change the newly created file from nesDS.ds.gba to nesDS.nds
3. place the aformentioned file and games into a folder on your SD
4. put this SD into your NDS and run nesDS.nds through the SC menu
5. load a game via the file menu on the touch screen
6. finger the touch screen for the in-game options
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