MATX are ok, unless you're an overclocker (they don't tend to fare too well with high FSB speeds) yeah you can't use as many expansion cards (but do you have that many?).
As to your processor being outdated. Its still reasonable for day to day things and ok for game performance, but the charts over here show just how much its bettered by the new core 2 duo line:
Chart the first,
Chart the second
These charts are with all processors equally clocked at 2.4Ghz, so even if you increased the P4 to 3Ghz (aka your current processor), and compared it to the entry level core 2 duo (1.8GHz), you still would have better performance with the core 2 duo.
Its all about how much money you want to spend. If you can justify spending the cash to get all new things now then I would really recommend it. But if not, then it might be best to just stick to what you have and get an AGP card and then start saving for a new rig. I'm going to say that its not worth getting the new mobo now, as although that will give you more options to upgrade your graphics in the future, your CPU will hold back the card too much to warrant getting the next card without a CPU upgrade too, which means a whole new setup next upgrade time.
For an idea on how much your processor would hold back the graphics card by (the percentage gap is probably more comparable to your next upgrade, i.e. not the 7900GS/X1950Pro your looking at now but the one after that) (although there will still be a slight holdback caused by your CPU in the case of the 7900GS/X1950Pro, but not as drastic as this chart shows)
Chart Graphics
Your CPU and a Core 2 Duo E6400 are highlighted.
I know the stats I'm showing you are more than likely me trying to convince you to upgrade everything now, but only go for what you can justify to spend. Provided that your PSU is big enough and you are happy with your current hard drives, you could get a new rig (graphics included) for ~$450.
So, decide...
Dan