The weakest guarantee you should settle for in the mail-order market should include:
72-hour burn-in to avoid that sudden infant death syndrome. (Also, try to find out if they do a power-cycling test and how many repeats they do; this stresses the hardware much more than steady burn-in.)
30 day money-back guarantee. Watch out for fine print that weakens this with a restocking fee or limits it with exclusions.
1 year parts and labor guarantee (some vendors give 2 years).
1 year of 800 number tech support (many vendors give lifetime support).
Additionally, many vendors offer a year of on-site service free. You should find out who they contract the service to. Also be sure the free service coverage area includes your site; some unscrupulous vendors weasel their way out with "some locations pay extra", which translates roughly to "through the nose if you're further away than our parking lot".
If you're buying store-front, find out what they'll guarantee beyond the above. If the answer is "nothing", go somewhere else.
Ask your potential suppliers what kind and volume of documentation they supply with your hardware. You should get, at minimum, operations manuals for the motherboard and each card or peripheral; also an IRQ list. Skimpiness in this area is a valuable clue that they may be using no-name parts from Upper Baluchistan, which is not necessarily a red flag in itself but should prompt you to ask more questions.
There are various cost-cutting tactics a vendor can use which bring down the system's overall quality. Here are some good questions to ask:
If you're buying a factory-configured system, does it have FCC certification? While it's not necessarily the case that a non-certified system is going to spew a lot of radio-frequency interference, certification is legally required — and becoming more important as clock frequencies climb. Lack of that sticker may indicate a fly-by-night vendor, or at least one in danger of being raided and shut down! (For further discussion, see the section on Radio Frequency Interference above.)
Are the internal cable connectors keyed, so they can't be put in upside down? This doesn't matter if you'll never, ever ever need to upgrade or service your system. Otherwise, it's pretty important; and, vendors who fluff this detail may be quietly cutting other corners.