The usual way people upgrade between revisions is to buy the newer revision, shift any hardware over that they want to keep (like a high-end graphics card), wipe the drives & reinstall MacOS X, and put the old machine up for sale locally or on eBay. Unless you live nowhere near a major metropolitan area, you won't have issues reselling the machine if you want to. Every time there's a new model, you usually see a bunch of folks selling their old systems.
The logic board may be interchangeable between different systems, but you're flying in unknown territory with that one - the logic board is tightly integrated with / customized to a lot of other components in the chassis (front panel controls, power supply, etc.)
Since Apple only sells parts to Apple Authorized Resellers and their technicians, your only option for purchasing a logic board (or replacement non-standard PC components) would be through ebay or a handful of used-mac-parts companies (like iFixit.) They buy new or used systems and disassemble them for parts.
CPUs on systems with socketed processors have some upgradeability; people have upgraded their Mac Pros this way (some Mac Minis and iMacs also had socketed processors, too) and documented as such on the usual Mac-related web boards/forums. This is expensive on the Mac Pros, given they're Xeons.
There should be no need to upgrade the power supply; they're reliable and designed to handle the maximum capabilities of the machines, which include some pretty 'big' GPU configurations. No, you can't pop an ATX supply in.
Depending on which generation of Mac Pro, the memory is specialized; some take FB-DIMMs. There have been reports that some aftermarket ram modules don't work well in some Mac Pros (temperature/heatsink issues), but a major manufacturer/reseller like Crucial should supply working memory.
Drives are completely standard SATA. Same with CD/DVD-ROm drives (verify the drive model works with OS X first.) There's an optional hardware RAID controller card that's probably not worth it. Areca, Adaptec, and others make compatible RAID controller cards; if bootability is important to you, check on this, as not all of them are.
Graphics cards are standardized for the most part (save some which have custom connectors; for example, mine has a DVI port and a mini-displayport.) The question is compatibility with MacOS X, but there are a very large number of compatible cards, and the Hackintosh community has pretty thoroughly documented that one for you already.
Sidenote: consider an iMac. It can drive a second display out of the box, they have a second internal hard drive bay, the i7's are as fast or faster than the Xeons in some applications, and they're a LOT cheaper than a Mac Pro; probably quieter and use less power, too. Spend the $ on more memory or an SSD, etc - an iMac with an SSD will wipe the floor with a Mac Pro without.