I detailed a few hacks/hacking techniques and so have a few others but there are a few things that are normally done.
SDAT/sound replacement: originally done to shrink roms (goldeneye has an especially small file) but these days is done mainly for undubbing games.
The simple undub merely takes the Japanese sound files and replaces the ones from the Euro or US release and it works most of the time. Other times there are extra or fewer sounds or it is done in a different order (the DS can use name of a file or ordinal (numbers) to call a sound) leading either to odd sounds being played or to crashing. Here you have to alter the files to match with techniques detailed in the next paragraph.
SDAT tweaking: various people have tweaked tetris to play different songs. I did it to play the classic tetris theme (
http://gbatemp.net/index.php?showtopic=36870 ) all the time and mufunyo removed the BG music entirely (
http://gbatemp.net/index.php?showtopic=69603 ).
Other times this can be done to reduce loading times/increase stability. Various people did it but it was kenghot who put out the patch you will most likely see for the Castlevania portrait of ruin.
Full blown sound replacement: the first people to do this were messing around with electroplankton as it uses plain windows compatible wave files which brings me onto the next thing.
What sound files are.
The most common format is the SDAT format. Used in all but around 10 games (unfortunately those 10 games are somewhat noteworthy).
Others use common formats (electroplankton) and not so common but common in games world (the world ends with you had a topic the other day
http://gbatemp.net/index.php?showtopic=86998 ).
One or two use tweaks on a "common" format meaning you will likely have to make new tools/alter existing ones to do it (lower bitrate/only mono audio/lower sample frequency/lower bit depth.....) but this is fairly rare and most tools allow for this even if they were not intended to be used for it).
SDAT format stuff is fairly easy to work with.
Specs here
http://loveemu.yh.land.to/page/NDS/SDAT.html
http://kiwi.ds.googlepages.com/sdat.html
Tahaxan forums have a early stage repacker but I find a hex editor and a spreadsheet nicer to work with.
For the BG music tweaking the file system is normally tweaked to read a different file (or none at all, normally by "reading" outside the actual file).
Next is simple replacement/swapping. I mentioned the repacker and it is easy enough to swap from rom to rom but the formats used within SDAT are not quite common PC formats which makes converting to the format a bit harder. The formats are detailed properly in the links I gave you above and kiwi.ds also made midi2sseq:
http://kiwi.ds.googlepages.com/midi2sseq.exe
You have simple sounds: drum hits, a gun shot in soundbite format (normally some form of PCM/IMA-ADPCM)
You have midi type files (not actual midi but close enough for conversion to and from) with their instruments in distinct sections.
Lastly you have full blown tracks (Tony Hawks games are the most common here). PCM or IMA-ADPCM (also detailed above) are the most common.
See the rom ripping and enhancements link in my signature or I also added it to the rom hacking docs also in my signature (and stickied at the top of the forum) for methods of pulling roms apart.
Threads you might find interesting:
http://gbatemp.net/index.php?showtopic=88172
http://gbatemp.net/index.php?showtopic=33647
http://gbatemp.net/index.php?showtopic=82825
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