SNEmulDS is the best for SNES, though it does still have graphical issues for many games. You can tweak the settings quite a bit if you're patient enough to test lots of options, and the PocketHeaven wiki has a compatibility list that has some notes for specific games.
For Megadrive, the best is jEnesisDS. The left and right sides of the screen are chopped off (due to limitations of hardware rendering), and a few select graphical effects are not emulated properly, but for the most part it's a solid emulator that will be able to play most of your games acceptably.
For PCE, to my knowledge nobody has made an emulator for the DS yet. You've got PCE Advance for the GBA, but that requires you to have a slot-2 device to run it. I have no experience with this emulator myself.