First BIOS and firmware are not the same thing on the GBA and DS- the BIOS does have a bunch of functions useful in system general and general operation (we call them BIOS compatible compressions for a reason) and to the best of my knowledge they (DS ARM9, DS ARM7 and GBA) are stored on a ROM chip. Possible hacks aside (and given we have total control over the DS it is pointless) I do not see the need to overwrite the BIOS.
The firmware on the other hand is somewhat rewritable though on the DS and DS lite there were no real projects aimed at incremental updates. The three mods were
Flashme - a hacked version of the original BIOS to remove RSA checks on download play components, allow force booting of GBA or DS slots (there was a time where the DS slot stuff was not properly understood), a little bit of PWM to vary the brightness level on boot and for some original models of the DS that had the lite's variable brightness chip for them to have variable brightness. Arguably the one most people used.
Loopy's minimalist firmware. Basically what it says and was the minimal thing needed to boot.
FW Nitro - the only serious attempt at a proper modded firmware as far as I know, kind of geared towards GBA slot stuff so not really so workable today where everybody mostly used DS slot stuff. It should be open source though so you might gain something-
http://fwnitro.caitsith2.net/
Tools of choice
http://nocash.emubase.de/gbatek.htm#dsfirmwareserialflashmemory and the docs at large.
Noflashme is the software method of rewriting the firmware but you will want a hardware one too and
http://www.darkfader.net/ds/ has you there (page search ppflash - you will need a parallel port).
Finally the original DS firmware is a hodge podge of many different compressions, encodings and whatever else (for example it uses BCD at points) so you might want a nice tool to unpack the lot. One unpacking tool-
http://forum.gbadev.org/viewtopic.php?t=12270 , it does not repack it but source code it there and the compressions are well understood.
There are a handful of tools that can also edit the DS firmware dumps to change names and whatever else (I tend to use crystaltile2 myself).