I've looked into Temper before trying this, and it had support for ISO/OGG/CUE. Not on 3DS though, at least from my attempts to convert them. Then again, I haven't tried again when the new versions showed up, but I see little point in that if ISO/CUE (or BIN/CUE) is considered better than using WAV anyway.
Yup OGG is supported in the original Temper codes. But I haven't enabled it and I'm not yet sure if the 3DS has enough power to decode OGG files. Exophase did suggest in an earlier post that the OGG decoding could be done in the 2nd 3DS processor core.
The new versions (v1.00b) also doesn't support OGG at all.