Some quick instructions from dantheman

I've packaged these together because Loopy removed these files from his website after releasing the DLDI versions of the emulators.  However, for devices without DLDI support, this is the only way to get playable NES and SNES games.

NES DS
This is using emu_kidid's unofficial builds.
Run make_nds.bat, add your games, click Save and use the default nesDS.ds.gba filename.  
Since ndstool.exe is located in the directory, it will produce nesDS.nds as well, which should be less than 3-4 MB for it to work.  
Put nesDS.nds on your card and run it.

SNES DS:
Grab the updated snesadvance.dat SuperDAT file from the PocketHeaven boards (current one is dated 6-28-07).  
Run make_nds.bat and add ONE SMALL GAME.  
Save as the default snesDS.ds.gba and it will produce a snesDS.nds file due to the presence of ndstool.exe.  
Ensure the final product is less than 4 MB in size, and put it on your card and run it.  
The produced *.nds file should run in no$GBA if you wish to test it.  
Because the final compilation must be less than 4 MB, large games like the DKC series will not run.

Credits:
Loopy for making these emulators.
DarkFader for making NDStool
mog123 and acelightning70 for maintaining the SNES Advance SuperDAT