dpgenc included with moonshell is fast and easy. batchdpg makes for some better quality with a bit more control and will let you encode in batch (ie: put files in que). i have never used SUPER but i have read that people get good results with it.
i get the best quality by using nandubmod (a fork of virtual dub) to remaster video with simple filters (both mpg and avi) then save out and encoding using highquality settings in batchdpg. i just encoded a dvd rip of the goonies and it looks great on my nds screen.
try all of the apps and see what works best for you. in the end it will come down to the source of the multimedia and how much effort you want to put into it.
-another world