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I'm going to be upgrading to a G5 and I'm a bit confused about the PCI architecture on the G5.

I know it's PCI-X.

Can I run my older PCI cards in this machine, or do I need to upgrade them all?

I'm currently on a MDD G4 Dual 1.25.

It's PCI-X depending on the G5 model. You can run 3.3 volt and 3.3/5 volt universal cards. You can't run 5 volt cards though, bzzzzzt. Check this... http://docs.info.apple.com/article.html?artnum=86513

You need to get an upgrade at https://secure.motu.com/store.html It's called a PCI-X 424 g5 upgrade.