The weakest guarantee you should settle for 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 as "through the nose if you're further away than our parking lot".
If you're buying from a dealership or superstore, 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. 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:
Is the memory zero-wait-state? One or more wait states allows the vendor to use slower and cheaper memory but will slow down your actual memory subsystem throughput. This is a particularly important question for the cache memory!
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 FCC sticker may indicate a fly-by-night vendor, or at least one in danger of being raided and shut down!
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.