another, higher rev. G3 board will be an exact replacement for the board that's in it. The only reason I can see to upgrade the logic board itself is to get a slightly better version of the onboard video chip.
You can upgrade the ROM to get both master/slave recognized on both ATA channels, and upgrade the CPU. Both are replaceable independently of the mobo.
I don't know if there are any other Mac logic boards that will fit in that case.
Add in a PCI USB card and you get access to all USB peripherals, but the USB keyboard and mouse aren't recognized until the OS loads the extensions.
Add a PCI video card, and you can use just about any monitor you wish.