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I think you can find a computer for the same price as you would get by building it yourself if you buy a used or refurbished one. I've bought tons of computers from ebay and from Gateway refurbished department. I have had good luck with all of them, and usually get something that's less than a year old for about half price. I can't recommend it enough.
It eliminates a lot of time with a screwdriver and such on the floor, at least.
Me - looks like it'll cost $X to do it myself, plus an afternoon with a screwdriver. Guess I only consider bids that aren't much more than $X.
Major mail-order places: "We don't make that, therefore you don't want it. We will, however, sell you this configuration with several components you specifically refuse to consider for half again what you are prepared to pay."
Whitebox builders: "We can do that for about $X." Some more, some less, but usually not by much. either way. They get the parts cheaper than I do, so they're still making a profit, some of my money goes to support local businesses so that they'll be there when I need a $5 cable or such, and I get a guarantee that's at least as good as it would have been to go buy my own stuff.
Some whitebox builders are truly pathetic, and I wouldn't want to own anything they built. I typically know that ahead of time and don't even ask them for prices. More often, though, I've found that I get what I want from someone who knows who I am and is motivated to keep me happy. Two years after I last bought a machine from her (or at all) I can still call up the woman who built my best machine and she knows who I am and what my machine's specs are. And she came in under what it would have cost me to do it myself. If you can find a good local builder, go with them!
1) Choose the OS first, that way....
2) You can go to the OS website and see what hardware is
compatible with your choice of OS. This might save both
time and money. This also works if buying new or used
parts or complete systems.
3) Whatever you decide to put on the public internet,
be aware that if you admin the server (i.e colo or dedicated
rather than a managed or shared server), you get to do all
the security related work. Can be time consuming and take
a lot of knowledge. Cracked servers are a menace to everyone.
Might want to consider FreeBSD or OpenBSD in addition to Linux.
After you get it working, you need to keep both the OS and
the application software (i.e. Apache & Co.) up to date.
FreeBSD has a wonderful ports system for keeping everything
up to date easily over time; check it out at freebsd dot org.