Quake DS doesn't require more than 16 MB of RAM, so you should be good with the 3in1. The Quake DS creator stated that from his experience, the 3in1 contains the fastest slot-2 RAM available, which plays a major role in the playability of Quake II DS, not so much in Quake I DS. Note that I haven't tried either of these personally, but I have a Supercard, which has the slowest RAM available.
For other homebrew the speed of slot-2 RAM really doesn't make much difference.
EDIT: If you're at all interested in DSLinux however, your main concern should be the amount of RAM, not the speed. In this case, more = better so the M3 would be your choice. If you don't care about DSLinux, 16 MB should be more than enough.