There are several things you'll want to think about when you get down to the nitty gritty with the hardware you wish to utilize... Theres many options, and even more options when you get to thinking about storage...

My personal recommendation is:
Slot 1 - Supercard DS One (Pass Through + MicroSD Storage Device).
Slot 2 - Supercard Lite Rumble Edition (Rumble Pack + MicroSD Storage Device).

For some people, the SC Lite Rumble may not be a good solution, for one it doesn't have the 32mb built in memory which allows utilization of Advance games. However, the DS One can utilize the rumble features of the SC Lite Rumble and you'll have additional storage space (since MicroSD cards can be 2gb, you'll be looking at 4gb of storage).

Another option for your Slot 1 would be a standard passthough card (SuperCard would be my recommendation as it is actually what I use and it works great). You may want to think about going with the SuperCard Lite vs the SuperCard Lite Rumble so that you can play Advance homebrew however.

An option for Slot 2, as mentioned above, is the SuperCard Lite, the standard version has built in ram so you can play advance games and home brew, the rumble pack version does not have this luxury.

In order to play any nds home brew or games you'll have to have some sort of passthrough device (slot 1).

For card readers, I highly recommend the "LINKSKEY LKA-CR811", it's one of the highest TransFlash (MicroSD) compatible card readers, and is quite affordable (at $4.99); I've used other options and they tend to fail quickly and be quite flimsy (in fact, my old one I had to use a pair of twesers to pull the sd card OUT!).

For media, I myself chose " A-DATA 2GB MicroSD Flash Card", for 24.49 it was a steal for 2gb... Now if the SD Reader in the DSOne or Supercard Lite supported MicroSD HC I'd have gone with an 8gb disk (at about $80) but they don't currently have any that do. This little A-Data card works flawlessly; and with 128 ratings (and a full 5 stars) it beat all of the other options hands down (not to mention, was one of the "better priced" options).

Some people complain that some MicroSD cards not being able to run some games when a certain capacity is reached; I haven't see this occour with my setup; in fact I am utilizing 1.7gb of my card and can still execute my 60+ games without a problem on any of them.