It's true, most skimmers that LFS's carry are not up to the quality of what you can get for a similar price online.
I've build a few DIY skimmers and mods dozens. If you're planning to use a DIY skimmer on anything larger than about a 29 gallon tank I wouldn't recommend it, and even then it's cheaper just to buy a used skimmer.
The biggest issue in building a skimmer is having the right tools for the job. In order to get the best performance, some amount of acrylic bending and cutting is going to be required, and most people just don't have access to those type of tools. A quality skimmer is much more finely tuned and developed than most people think. The pump, venturi size and length, air-intake, reaction body width and height, neck width and height, as well as collection cup dimensions are all unique even though many skimmers look similar.
It much easier, and only slightly more expensive, to buy a high quality skimmer such as an Octopus, Euro-Reef, or ASM than it is to DIY a skimmer of equal quality. Trust me, I know from experience...
Well, i've you're really set on DIY'ing one. What type are you thinking of? In-sump or external? What method to achieve the fractionation, needle-wheel, down-draft, etc?
The most difficult part, in my opinion, was creating anything that required o-rings to prevent leaking, such as the join between the neck and the collection cup. It's extremely hard to make parts to such a small threshold of error to provide a water-tight seal without some high quality tools. I went with a Twist-and-lock method made out of 1/4" acrylic similar to the one beananimal has on his website. I was never able to get it completely water tight. You could buy a twist-and-lock flange, but last I check they run pretty pricey, and that defeats the purpose of a DIY...
Most of the time, when I do a DIY project it is not to save money so much as get a custom fit or function. That said, other than the tooling issue that The0wn4g3 mentioned, the other obstacle with a DIY skimmer is the material minimums. Typically, in order to buy acrylic pieces at a cost effective price, you have to buy a bunch of it. That's not a problem for large projects or multiples, but a single mid-size DIY skimmer will be expensive. It is fun and rewarding though.