There are several Electroplankton that can use the microphone for input. Nanocarp responds to claps and note patterns. Volvoice warps a short recording through a variety of filters. And Rec-Rec, which is rapidly becoming my favorite, actually acts as a four-track tape loop with variable speed, all fed from the microphone input.
However, if you're really interested in using Rec-Rec musically, you won't want to use the built-in microphone. It's too noisy, too weak, and positioning the console for use and recording simultaneously is much too difficult. Instead, you need to access the front headset jack that Nintendo has thoughtfully built into the DS.
Now, as far as I am aware there are no adapters for the headset jack available in the US as of this time. The only commercial possibility I've found (which might be vaporware) is here, but would require you to mail-order it from England just to cut it apart. Even so, don't set that possibility aside just yet.
Your other option, until headsets become available domestically (my guess: possibly soon, with Nintendogs out, but more likely at the end of the year when Animal Crossing and Mario Kart hit), is to make your own adapter. This is not hard, especially if you know how to solder, but you do need to be careful. Both the onboard mic and the headset jack share a circuit, so if you short one you will also short the other, and then you won't be able to use any microphone input.
So in order to run my bass into the DS, I just bought a standard 1/4" jack and some wire. I soldered mine together, but that's just because I'll take any excuse to break out a soldering iron--those who don't want the hassle can use a crimp-style connector, or possibly just buy a guitar cable and cut one end off. That's the easy part. The hard part is finding a way to make the connection with the contacts inside the DS mic port that A) won't touch the wires together, creating a temporary short that transmits no sound, and B) will make reliable contact, possibly staying put even if the DS is bumped or carried around. My first attempt at a solution was to buy a set of motherboard jumpers, which looked to be about the right size to hold the ends of the wires. Unfortunately, the port is just slightly too narrow.
Reading comprehension test: under no circumstances should you try the bare-minimum approach shown in Figure 2, which is just the wires looped over and jammed into the mic socket. The reason for this is that the contacts for the socket are very, very delicate. Really, they're just thin metal leaves. If you bend these contacts too far with brute physical force, you will short the entire microphone bus, and no audio input will be possible at all, although everything else will still run fine. This is, of course, exactly the mistake I made. In order to fix the short, you'll need to have one of Nintendo's crazy three-pointed screwdrivers (available from Lik-Sang), and even then the port may be flush with the motherboard in a sealed assembly--I can't tell from pictures of the internals. Since I don't own the screwdriver and at that point didn't want to risk any more damage, I took the DS to an EB Games and traded it in for a new one. Clearly, this requires not just a tolerance for blatant dishonesty (or as I prefer to say, contempt for The Man), but it'll also run you some cash for the trade-in value. Either way, it's not a satisfactory outcome.
The whole debacle makes me unlikely to try such a connection again right away, but if I were to do so I would stress using materials that will give easily, and won't force the contacts. You might try using thin stranded wire, but keeping the hot and ground separated will be difficult. Another option is a set of metal leaf contacts similar to the DS's own connection, but you'll still need something to hold the wires. That's why I stated above that you might not want to immediately dismiss the idea of importing Big Ben's headset if possible, as linked above, and tear it apart for your audio connection. It solves both problems with a homemade adapter: the contacts are safe, and the integrated earphone connection keeps the whole assembly firmly attached.
The worst part of it all is that I had a lot of fun using the microphone input before I realized the problem I'd caused. The DS either has a very hot preamp or expects very low-powered input (more likely) because my passive single-coil bass was almost overdriving Electroplankton, and my pickups aren't that loud. You might have to put a volume pedal at the end of the signal chain to bring it down, particularly if you're using effects like chorus or distortion. Once the volume is at the right level, the signal is fairly clear, although it's hardly going to be hi-fi. A more sophisticated adapter (or someone with a better soldering technique) might get better returns.
If you have better luck accessing the microphone, or you know of a better way to put this together, please let me know in the comments or by e-mail. As we'll see when I finish putting together my Rec-Rec article, the ability to record directly into the DS is probably key to Electroplankton's most powerful tool.