For O3DS? Well, you have the choice of rxTools, Cakes, and Pasta. I say (and still say) to go with whatever suits your needs best. If you need a lot of fancy tools for dumping NANDs and ROMS go with rxTools. If you just want a simple emunand, go for Cakes, or if you don't want to use an emunand, and prefer to do everything on sysNAND for whatever reason, use Pasta (I personally don't recommend this option though, I see Pasta more as a tool for upgrading to 9.2 so you can use themehax!).
Disclaimer: I don't own an O3DS anymore, so I'm just going based off what I have seen of those 3 CFWs.