GUI apps do not really exist yet (there is a NSMB level editor, deufeufeu made some stuff for some of his projects and there is a couple of FF3 tools when it comes to the DS and the GBA does not fair much better:
http://www.romhacking.net/?category=&P...itle=&desc= ).
Others have mentioned the file system and I agree. Unlike most other cart systems which have the binary and files all together the DS has files able to be distinguished from each other.
There are multiple apps for this including
ndstool (command line tool which is part of devkitpro and has the .net using frontends DSlazy and DSBuff, my signature on rom ripping has links and batch files to use it). Some carts/roms do not play well with it though.
NDSTS: made by the same guy as GBATA. Only able to extract and replace same size files.
Nitroexplorer (probably the best alternative to ndstool and co). Made by treeki (same guy as the NSMB editor)
NDSHV: site has been down for ages but made by Vinpire if you want to go looking.
And you can alter it yourself:
http://nocash.emubase.de/gbatek.htm#dscart...roromfilesystem
At the most basic form this enables swapping of files (see undubs and early ripping of roms to fit on small carts as well as the wifi hacks) but it forms the basis of all DS hacking.
Furthermore the files themselves often have similar file systems/layouts (usually a 4 character identifier followed by size and location of useful data) so you can usually hack them (if you are lucky someone will have already figured out the format). Of course not all formats are documented (and those that are can be changed or incomplete: early NARC (a format a bit tar files that can store just about anything) files/documentation did not have directories accounted for and so did not work so well when directories appeared).
Oh and the rom hacking stuff in my sig/stickied at the top of the forum should help get you some links at least.
As for mario (NSMB) the text is basic unicode (I did some hacks way back) and the levels have an editor:
http://www.romhacking.net/?category=&P...itle=&desc=
Other mario games can be a bit harder as they favour compression (mainly bios compatible LZ but it can be a pain to work with).