I'd say the best PPC Mac will depend on exactly what you want to do on it.

Fastest that can natively run OS 9 with full driver support is going to be the MDD.

Best low cost and low space for tinkering is going to be the mini with the caveats you mentioned.

Best price to performance on the used market for PPC OS X software is probably an iMac G5.

Absolute best performance for PPC OS X stuff is going to be the PowerMac G5.

Honorable mention to the eMac, which can be be found for ~$100, 1ghz combo drive models and below can natively run OS 9 with full driver support or you can go with up to the 1.42 ghz model which is going to be similar to the fastest G4 minis, and comes with a beautiful built in CRT, with the caveat that it takes up as much space as a CRT.