Mic has updated his Nintendo DS Emulator for windows, heres whats new:
GPU: Added support for the A3I5 and A5I3 texture formats
GPU: Fixed some errors in color selection for paletted textures
MMU: Upped the FAT limits to max 32768 files/directories with a total size of 256 MB
MMU: Added support for long filenames in the FAT
GUI: GBAMP emulation can be turned off (on memory tab, or in dualis.ini)
GUI: Switched from WM_TIMER to a multimedia timer callback
Note that the max number of directory entries at the root level still is 512, and that the max total number of files/directories will be lower than 32768 if there are files that uses long filenames