DS2DS can send files between DS's, provided they both have it working. As for some other apps...
-Moonshell2
-Morning Timer
-Comicbook DS
-Image Viewer
-Cooking Timer
-Animanatee
-DSMetronome
-MarioPaintComposer
-MorseDS
-NitroTracker
-NeoDS
-SNEmulDS
-SenoDS
-Innocence
-VNDS
-Homebrew Menu
-PPSEDS
-DiagnoSe
-StopphurDS
That is all I can think of at the moment.