What methodologies do you use to decide on which parts to buy?
I first determine the machine's purpose. A development machine has different usage than a gaming machine, which has different usage than a server machine, which is different from a home user.
Starting from the usage scenario, and a budget, I look at what's available at what cost.
In selecting parts I generally look for the point where you're not getting the cheapest stuff (which is only a little cheaper than midrange) but is below the most expensive stuff (which has only a little more performance than midrange. It's not exactly in the middle - for some parts it's worth making a chart of cost/performance (or other metric which is important for that part) and seeing the part of the curve where you get the most bang for your buck.
Then I make compromises based on usage and cost.
Do you look at benchmarks?
Yes, but only peripherally. I use them primarily to make sure there isn't' a huge disparity between price/performance for a given component, but beyond that in this industry you generally get what you pay for in the mid-range.
For some usage scenarios it's important to take this into account, as certain usage may have critical requirements, such as when selecting between a hard drive and an SSD. SSD is better in most cases, but for a few usage scenarios a few cheap hard drives in raid is better because raw sequential access is more important than seek time.
Do you find things that have compatible bus speeds?
As long as the buses are compatible, then I'll optimize to requirements and cost. It may be vastly cheaper to go for the slower RAM now, and upgrade later if/when needed, even though the ram is slower than what is possible.
How do you know where to look to make sure everything will be compatible?
Only at the bleeding edge (very high end/high cost/newest) is this actually important.
In the mid range (best bang for the buck) the hardware has been out for months, has had at least 2-3 revisions, and has stable drivers. This isn't an issue unless you're using the latest and greatest MB, video card, OS, etc.
Do you buy a bare bones machine and extend it?
I buy my components individually and assemble it. Barebones machines, when I've done price comparison, are often not as good a deal as they appear to be at first - they usually make some small tradeoff. An equally good deal can be found with the parts you actually want with careful shopping.