StellaDS v0.5 (the Atari 2600 Emulator for the DS) has just been released. Here is what is what Thechuckster had to say:

Currently there are precompiled NDS ROMs with a potluck (what ever I feel like testing my emulator with ATM) 2600 ROM built-in. GBFS support and a multi-ROM menu will be added in the near future. The source code is also available for download.

Unfortunately, a project compiled with ARM7+ARM9 combined binaries only yields an NDS file with Devkit Pro. Get a loader if you are using a flash cartridge. Sorry.