So I currently have a G4 MDD dual 1.42ghz Mac with a reflashed for mac compatibility Geforce 7800gs gpu. I'd like to give Morphos a try (mainly to play 720p MKV files, since OSX fails horribly at this) and was wondering what my options are as far as compatible gpu's go. Could I just add in a PCI gpu with a compatible chipset and use it for Morphos while still using the Nvidia card for OSX? If so what would be the best PCI card to go with? Would it need to be a Mac specific version? Anybody on here run a similar setup? If so, how's it working out for you?

In AGP terms the fastest GPU actually supported by MorphOS (both 2D/3D) should be Radeon 8500/9100) but soon (MorphOS 3.0 "should" be released before the end of the year) the Radeon 9800 (they made also XT Platinum edition..) should be the absolute faster GFX Board supported by MorphOS. I don't know how far in performance is from your 7800gs (if not a big difference you could use just one AGP GPU for both Operative systems)

I can't aswer you about possibility to still use your Geforce + a PCI Radeon. Let's wait other answers.

P.S. Yes, the GPU must have a MAC BIOS inside. Many of us buy cheaper PC Radeon boards and flash them with MAC BIOS.

Forget about the Geforce, even if you have a Radeon in a PCI slot. Your fastest choice for MorphOS will currently be a Radeon 9800 (but it must have a Mac bios for working in the Powermac), but without 3D support, which is a subject to change in the upcoming MorphOS 3.0 release. But I don't know, if it will be enough for 720p movies on your setup.
My setup is a Gigabit with an 1,6GHz CPU upgrade and a modified Radeon 9250 AGP, and it's not enough for 720p. But your setup is a bit faster than mine, so maybe it will be enough. A Mac mini G4 with 1,5GHz is said of being able to handle 720p movies, so it's definately worth a try.