Just a note in regards to the G4 MDD, if it has a FireWire 800 port it can NOT boot OS 9. The MDD units that only have FireWire 400 ports were the last PowerMacs to boot OS 9, IIRC.
The folks over at OS9 Lives have been working on getting OS 9 on unsupported machines, and the FW800 MDDs were-I think-the first ones they "cracked."
The early technique was to downgrade the firmware to the FW400 firmware. As I recall, this disabled the FW800 port, but actually had the interesting side-effect of making the internal USB ports run at USB 2.0 speeds in OS X(they were actually USB 2.0 compliant but were artificially limited-my theory is that Apple wanted to push people toward Firewire for data transfer, and thus drug their feet on including USB 2.0 across the line). I think they now have an OS 9 install that will install directly on the FW800 MDD.
As a side note, though, I know that when I refer to the "MDD2003" I'm talking specifically about the FW400 version that Apple introduced at a VERY low price point after the G5 was announced. I've heard that it was done for OS 9 support, although I don't know how true this was. In any case, though, the majority of these computers are single 1.25s and make for great dedicated OS 9 machines.
As to the original question-I can tell you that Geekbench will score the single 1.8 G5 about 1.5x faster than a single 1.25 MDD. To be fair, I have the "original" Single 1.8, not the iMac in a tower version.
A dual 1.42 MDD can trade blows pretty well with a low spec G5, although if you're using software that can leverage the G5 instructions completely the G5 will come out ahead. Also, the super speed 7447A-based G4 upgrades don't really get competitive with the dual 1.42 until they pass about 1.6ghz. I have a 2ghz 7448 upgrade card in a DA G4, and it really only shows its speed in single threaded tasks.
There's a lot more to the G5 than just the processor-the entire system really can just move data around faster than the G4 towers and consequently I find even lower spec ones are often faster in general use. It doesn't stop me from using G4s, though. In fact, I only recently "retired" a dual 1ghz Quicksilver in favor of a dual 2.7 G5.