Applications:
DSlinux - ssh and best browsers on the DS ATM
Games:
Nethack DS - roguelike, now we need Angband
wanted to change game vote... and now final vote, below are the "honorable" mentions
DSOrganize - lots of useful functionality and good browser, but it wifi seems flakey
Arcomage - nice CCG from Might & Magic
QuakeDS - DS version of Quake
Powder - another roguelike, simpler than nethack
moonshell v1.71 - another general purpose app with a media application bent
dslibris - ebook reader
Rudolph's ExpPack Tool - essential for 3in1/GBA use