You can obviously do tons of hardware mods, case replacements, LEDs, PulseVU type things, etc.
As for the other kind of mods there are a few avenues to pick from.
1. Buy a slot-1 flashcart and not alter anything. Slot-1 carts work without any modifications to play NDS backups and homebrew. But, you cannot play GBA backups.
2. Buy a slot-2 flashcart and play a vast majority of NDS and GBA backups and homebrew. But you need to flash the firmware in order to get the DS to read from the GBA slot instead of looking in the NDS slot.
3. Buy both, and have the best of both worlds, and no need to flash firmware. Some slot-2 carts offer things such as rumble, or extra RAM for the Opera Browser, etc.
Personally, I went with option 1 and bought a DS-X and did not flash my firmware.
The cheapest, easiest and safest would probably be the R4DS and not flash firmware. You can brick your DS with a bad flash. But, if you get one good flash in, you should be set, because all current hacked firmwares have a fallback in the 1st few bits. So, if anything ever goes wrong you can easily reflash without worrying about bricking.
Here is a chart of Slot-1 flashcarts:http://wiki-scene.com/index.php?title=DS_Carts