I cover quite a few in the rom hacking docs at the top of the forum/in my signature. Those are some good ones.
Still
no$gba debugger is now free and has better debugging than desmume for a lot of things.
http://problemkaputt.de/gba.htm
http://code.google.com/p/tiledggd/ is a great graphics viewer.
As well as crystaltile2 there is tinke
http://code.google.com/p/tinke/
It approaches things in a subtly different way but that might work for you.
Hex editors I cover in the docs. If you want free than tiny hexer
http://filetrip.net/pc-downloads/applications/download-tiny-hexer-1-8-1-6-f29009.html ,
http://hexplorer.sourceforge.net/ and XVI32
http://www.chmaas.handshake.de/delphi/freeware/xvi32/xvi32.htm
As well as that you might want a rom hacking focused hex editor. Crystaltile2 has a good one, there are various others mentioned in the docs.
Games easier to hack than others... there are some. What are interested in learning to hack first? Text, 2d graphics, 3d graphics, music, levels, general gameplay styles, cheats, save editing....? I have not got one game that is easiest for all of them, however I can probably drum up some good stuff for one or more of them. Do you care about having a finished result? Figuring out how something works is most of what I care about, others do actually want to change the games.
Equally it is the little fiddly things that keep most ROM hackers coming back.
Music wise for the DS the main sound format is called SDAT and it is used in most games (as in with region dupes you are probably going to struggle to hit 50 without it). In this case you can pretty much pick any game and it will be good for learning the main aspects of SDAT hacking.
Text. I still reckon any game using BMG format (mainly Nintendo first party stuff, new super mario brothers being my main example).
Graphics. I could point you at a basic NSCR, NCGR, NCLR game but we even have viewers for those that work with regular graphics editors. 3d editing on the DS is odd (even the 3ds is more than advanced) so I am not sure what I can point you at. The main format is NSBMD for 3d on the DS and a good chunk of games that use 3d then use this, however editing it is not the easiest and tends to have to be done manually, or you make a model and use the leaked SDK files to handle that.
Levels, if you can follow along with
http://treeki.rustedlogic.net/romhacking/docs.html you are doing OK. N+ might be easier for some parts of it but not for others.
General gameplay. Normally I would suggest you learn cheats as far as giving people weapons, making moon jump, making walk on water.... sort of thing as it will probably also teach you what is happening in behind the scenes of a game. I can not bring to mind any games on the DS that you can edit ini files,
python scripts and start fiddling with the game that way. Maybe some of pokemon kind of has this but if I count that then I have to count an awful lot of games.
