The CF cards are much larger than the SD cards physically so they will stick out from your DS more. Also CF cards come as large as 8GB where as the largest SD card right now is only 4GB.
If you only plan to play Nintendo DS games then the Super Card should work just fine for you and is much cheaper than the M3. The Super Card only has problems with the GBA games not the NDS ones. If you plan on playing both GBA and NDS games then get an M3.
Also if you have a DS Lite you might consider waiting for the new G6 card that is going to be comeing out soon. It looks just like the Dust Cover on the DS Lite so you wouldn't even know it was there. It holds 512MB of highspeed flash Memory so unless you plan on watching movies or listening to alot of MP3's it should be large enough to hold most of your NDS and GBA games.
(http://www.maxconsole.net/content_img/g6lite3a.jpg) (http://www.maxconsole.net/content_img/g6lite3.jpg) (http://www.maxconsole.net/content_img/g6lite1a.jpg) (http://www.maxconsole.net/content_img/g6lite1.jpg) (http://www.maxconsole.net/content_img/g6lite2a.jpg) (http://www.maxconsole.net/content_img/g6lite2.jpg)