The best "official" GPU for these is the Radeon 9700, but good luck finding one. I know of three owned here in the MR community PPC, one of which(mine) doesn't work.
The 9600 Pro PC&Mac edition and the G5 9600 XT are also decent choices. Moving into a 9600 or better GPU, or an nVidia 5200 or better gets you Core Image support, which will make the animations and "eye candy" in Tiger and Leopard work a whole lot better and also free up processor resources. The 9600 PC&Mac will require installation of the drivers, but is otherwise plug and play. The 9600 XT requires taping pins on the card, but otherwise will work well(I use one in my Quicksilver, albeit with an additional modification to support an ADC display).
In PowerPC Macs, you need a card with Macintosh ROM. PC cards can be converted to Mac cards by "flashing" the ROM. There's a fairly large collection of ROMs available at this website
http://themacelite.wikidot.com/wikidownloads2
In most cases, a PC card will need to be "taped"(instructions are available on this). ATI cards can generally be flashed in safe mode in Tiger(you will need a PCI card to see what you are doing-a Rage 128 out of a B&W G3 or the like works fine). nVidia cards must be flashed in a PC and require finding the correct version of NVFlash(sometimes easier said than done).
All of that aside, the 9800 is a popular flashing candidate, although be advised that this card runs VERY hot. A popular starting source lately has been the ATI FireGL x3, which will flash very nicely into the equivalent of a Mac Edition X800XT(the second best AGP PPC card available). There are some other candidates, but the FireGL is an all around good option that will give you good performance and is very reliable in an MDD. It's the one I would steer you toward. There are sellers on Ebay who sell them pre-flashed, although I prefer not to support them as they are generally using the MacElite ROMs that are provided free of charge for non-commercial purposes.