The central fact about clone hardware that conditions every aspect of buying it is this: more than anywhere else in the industry, de-facto hardware standards have created a commodity market with low entry barriers, lots of competitive pressure, and volume high enough to amortize a lot of development on the cheap.
The result is that this hardware gives you lots of bang-per-buck, and it's getting both cheaper and better all the time. Furthermore, margins are thin enough that vendors have to be lean, hungry, and very responsive to the market to survive. You can take advantage of this, but it does mean that much of the info in the rest of this document will be stale in three months and completely obsolete in six.
One good general piece of advice is that you should avoid the highest-end new-technology systems (those not yet shipping in volume). The problem with the high end is that it usually carries a hefty "prestige" price premium, and may be a bit less reliable on average because the technology hasn't been through a lot of test/improve cycles.
There used to be a real issue with low-end PCs as well, because there used to be a lot of dodgy crap PC components out there going into boxes made by vendors trying to save a few cents. That's not really a problem anymore. Market pressure has been very effective at raising reliability standards for even low-end components as the market has matured. It's actually hard to go wrong even buying at the bottom end of the market these days.
I put together the first version of this guide around 1992; Unix-capable systems are now five to ten times cheaper than they were then. At today's prices, building your own system from parts no longer makes much sense at all —so this HOWTO is now more oriented towards helping you configure a whole system from a single vendor.