They're really very different animals. If you have to ask the question, you probably shouldn't build a Hackintosh as your primary work machine. That's not to say it can't be done, but until you've built one you have no idea what you're getting yourself into.
The best analogy I can think of is this: Buying a Mac Pro is like walking into your Harley dealer and riding off on a brand new hog. Putting together a Hackintosh is like building a custom chopper starting from a chassis and engine. Sure, they're both motorcycles. But they're not really even close to the same thing. The Harley is a highly engineered and tuned machine with components that are designed to work together*, and the chopper is an assemblage of individual parts that, with skill, patience, and a bit of luck, will run relatively smoothly. Of course, you get exactly the bike you want with the chopper (not to mention the coolness factor), but it's never going to quite be a Harley.
With the Harley, if you have any problems with it you take it back to the dealer and they fix it. You might be able to do a bit of maintenance on your own, but certain things are simply beyond your reach. For example, a Mac Pro at work just died suddenly, probably due to a bad power supply. With off the shelf PC hardware this is trivial to replace, but it's not something that can be fixed easily on a Mac Pro, if you can even diagnose that is the problem in the first place. But then, you don't have to worry about that, because you just take it back to Apple or pay someone to fix it for you.
With the chopper, you'll be intimately familiar with every component in the system. Which is a really good thing, because you can expect absolutely bupkis in terms of official support. Since it's your custom setup, a given component may or may not work correctly--or at all--and pretty much the only way to find out is to try it and see if it works. Even then, you have no idea about the long term reliability of the system.
Having built several Hackintoshes myself--my main desktop has been a Hackintosh of some sort for the last two years--I can tell you that it's never as straightforward as it might seem. Getting the system up and running is no picnic. There are no clear instructions on how to use all of the tools together to even get the system to boot OS X, and when something doesn't work correctly, you're left with little more than a cryptic error message, or just a consistent hang. Once you do get it working, you're going to have to learn about kexts, graphics strings, DSDT files, and so on just to get each individual component working. Software Update? Yeah, good luck with that. It might work, but it's just as likely to break something in some unexpected way. Also, there are weird bugs that will just surface randomly, even after you have everything ostensibly working. Some of these will be merely annoying (e.g., the system doesn't shut down properly after waking up from sleep) and some will be real hair-tearers to diagnose and fix, if it's even possible to fix them (e.g., ripping a DVD from a SATA drive causes random kernel panics, but only if you have more than 4GB of RAM installed).
Eventually, though, you'll most likely end up with one of two outcomes: a flakey computer that will give you no end of trouble on a daily basis until it ultimately dies in a spectacular way, taking part of your data with it; or a system that's reliable and stable, but somewhat fragile in that if you screw with it too much in terms of changing the hardware or mucking with the OS, something is more likely than not to stop working properly. I've built both kinds; in fact, my current hardware was previously the former under 10.5, but with the upgrade to 10.6.2 it has become rock solid. Even then, updating to 10.6.3 caused my sound card to stop working. I managed to fix it without too much trouble after searching through the incredibly helpful forums at insanelymac.com, but it was still an extra hassle that would not have been an issue on a real Mac.
The flip side of this is that you gain a lot more flexibility in terms of what you can add to the system. Off the shelf PC video cards? Sure, no problem. Stuff five hard drives in your case? Yep, and I've still got room to spare. Want a faster processor? Just swap it out. Of course, you'll still have to configure all of these things, and any one of them might not end up working, but on a Mac Pro, it would be impossible anyway.
So, the bottom line is that if you want a customizable system, want to learn about the inner workings of a Macintosh, have a reasonably solid grounding in Unix and the command line and computer building (or are willing to learn), and don't mind wrenching your system on a semi-regular basis, a Hackintosh can be a great choice and a fun learning experience. If you're looking for a computer for work, and can't face the prospect of having your computer potentially explode at any given time with no tech support available at any cost, then a Mac Pro would be a better choice.
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*Well, that's the theory at least...
