There are a few, such as many Gigabyte boards, that support PCIe x16 and AGP 8x, but they have their own issues. Anyhow, for that system you have, the biggest bottleneck would be that POS GeForce MX. My suggestion of getting a 9600XT will bring your machine as far as it can go. More ram would be pointless in most cases, a faster CPU would be a waste of time, and a new motherboard would require a replacement of everything, with exception of IDE and PCI devices. Your choices are to buy a new PC (maybe $700 for a relatively decent setup), or buy a 9600XT for about $100. Considering the cost, I think the latter is the better choice.
Anyway, to break it down:
Good 430W PSU - $65
Mid-range motherboard - $90
Athlon64 Venice 3200+ - $160
256MB X800 GTO - $170
2GB PC3200 2-3-3-6 - $235
This kind of setup is for upper mid-range machines by today's standards. Also, the figures are just to get the machine up and running. No hard drives, periphreals, monitors, etc are included in these figures. This $700 could easily turn into $1000 for a complete package. I hope that clears things up.