Chad, you only need to get so close. A set of plug gages will get you very close. If you're working from a print with tolerances, a go/no go will do you, its seldom that you get a hole less than .0005 tolerance, and most(most not all) of the time when you see that its because of an engineer getting their rocks off. Most of the QC departments I deal with realize that.
A set of Chinese pins is cheap. I've seen .011 to 1.000 for as little as $360. If you need to get closer or go bigger by a bit, you can use the 3 pin method. I have a spreadsheet at work that has it mostly figured out, I can e-mail it to you or anyone else thats interested. Its just easier than figuring it out each time.
Its pretty simple and can be done with a single set of pins, and using average size pin, it puts you off by a couple of millionths using pins from one set. Its a really easy formula, pen and pencil and in 5 minutes you'll have it. I learned this trick from a real smart guy I used to work with that pops up here once in a while.
As for the small hole gages, I'm assuming your talking of telescoping gages, personally, I think they suck. As TOOLMKR said, measure many times and take an average, then get somebody else to do it, and they will be off from your measurements, horrible little things, very very inconsistant. Good for a ballpark estimate, but I wouldn't trust them for any sort of accuracy.