I see you have encountered the 3d models and 2d sprites thing.
There are viewers some of the various formats and there was a leaked 3d SDK that I have no seen anybody do anything with yet. Certainly do not expect anything close to what we have for 2d formats or even some of the sound stuff.
3 formats at least (brothers in arms I think it was had another but I have not really looked at that game).
Metroid, very old and barely used. I mention it mainly in case someone else comes reading this for info about DS 3d formats.
http://nerdmentality.com/forums/viewtopic.php?id=10327
NSBMD. Nintendo SDK format and probably the most common.
Mario 64 DS had a precursor to this and some interesting stuff has happened there in recent months. I believe pokemon has something of a successor if not a fork/mod of it (pokemon games have a habit of this).
http://kiwi.ds.googlepages.com/nsbmd.html a bit old and a bit clunky/wrong in places but will point you in the right direction.
http://llref.emutalk.net/docs/ has a few more modern/complete ones.
http://www.romhacking.net/forum/index.php/topic,8407.html is a nice discussion on the matter.
3d is rather more complex than 2d on the DS so most developers will not rock the boat.
I also stumbled across this
http://nvwr.googlecode.com/svn/trunk/libs/formats/ the other day which might be of some use.
3d is quite large so assume compression at all times, mostly it is simple LZ that any tool can decode or at worst something like a CARC or NARC file (a simple container format). Do also remember 3d imaging is built entirely around tricks of the eye and other things to reduce load (especially on the DS) with texture swaps more common than palette swaps in final fantasy, tricks like NSMB where the signpost has the alt text on the back (a bit of rotation and it appears as though it is a new sign when not so much as a new piece of info has been loaded into the texture or model memory sections) and if it is possible to avoid rendering something it will be avoided (I am sure we have all had cameras peer through walls in a game before).
Still a knowledge of the DS 3d hardware is worthwhile.
http://nocash.emubase.de/gbatek.htm#ds3dvideo
I am not sure how I want to sell that. It is not that bad/complex
If you really want do poke around a couple of the homebrew 3d libraries as well.
Most 3d hacks for the DS are simple tweaks (the NSBMD format is simple enough and 3d graphics have a nice habit of being generated in hardware after all), camera tweaks (see some of the people toying with first person pokemon), same game swaps (filesystem hacks) at best from a beta of the game (a couple of people over at
http://www.dshack.org/forum/index.php?/forum/4-hacking/ took this to quite a high level although the 3d is so much window dressing with the track layout being the thing that most look for) although not all models (and their animation formats/abilities) are created equal. A sequel might work for this but I would not put money on it.
You are going to have to mess with
3d models
3d textures (some just use material colours so you might get to dodge this)
3d animation files. This for my money is probably going to be the trickiest- editing a sprite is so much copy and paste once you have the format decoded/sprite locations (the game itself more or less takes care of the rest unless you want to add or remove frames of animation) but 3d stuff is touching proper programming in some ways. Indeed I might look at some of the stuff in the music world as it is fairly similar logic (multiple play options which you need to match, jumps and calls to wherever else (not so bad if it is internal but if the game wants to start somewhere)).