Personal Favorites, still use them. They are top notch. (in no order)
x86 CPU emulator: Emulates old 268 dos games or even 386 if a supercard, great for testing/learning x86 ASM code! or for normal people to play games like Wolf3D, DOOM,etc (DSx86)
Fasttracker II: Nitro Tracker, make and listen to good music (think Synth style)
PocketPhysics: Fun Physics simulator, Lets you play with gravity!
Colors DS: Good drawing, great GUI, pressure sensitive.
GameYob: Great GB/C emulator, near perfect
SNEMULDS/
LOLSNES: SNES DS Is better but not for long, lolsnes will hopefully emulate DSP1 and make me happy.
XENOFILE: anything the ds can do, is here. universal file manager, and loader. needs moonshell installed, as it uses moonshell plugins in addition to its own.
more moonshell plugins(AVI/GBC/GBA/NES/etc). Polished feature wise with ARGV and EXTLINK loading, gui could be better though.
There are manyyyy more good homebrew out there, a google search helps out. also Filetrips NDS section is helpful. It all depends on what you want to get accomplished or do. There are even multiple browsers for the DS that work quite well or Win2DS. Or drawing tools that let you export .avi of animations, playable in tuna-viDS.