Generally speaking there are two types of bikes for sale on Craigslist. The first type is one with a manufacturer name, model name, and date of manufacture. The second type is the bike that doesn't have those identifiable characteristics. These second-type bikes might be called custom.
If you have a manufacturer, model, and year then you can use bicyclebluebook or just do some napkin math. My rule for bikes is that a used bike is worth half of what a person paid for it. That's a harsh rule but it runs true in my market. For these first type bikes you are going to have a general idea of the original value of the bike and then it is up to you to decide how much you want to pay for the bike you are looking for. My recent experience is that once I found out what I was looking for I started to see the same makes and models come up and similar price points. I would miss certain bikes at certain prices and I kept an informal idea of that those quality/value/price points were; aware that if I saw a similar combination anytime soon I would jump on the deal.
The fact that you apparently haven't checked out any bikes on Craigslist seems to indicate that you haven't really started looking yet, that you are pre-looking. I propose that once you start looking, and look for a few weeks, things will start to click. You are not going to figure this out in a few days!
As for the "custom" bikes it seems like you have a general understanding of at least the fact that there are differences among frames and among components. For pricing these things I tend to check ebay completed listings to figure out what things are selling for. You could literally add up all the used parts and you should be close to what a bike made of those parts should cost. I might get blasted for proposing this but the economics tend to work out for used bikes in the $500 - $1000 price range assuming discounts and premiums for condition and rarity. The range of components across manufacturers and types of bikes is HUGE. But as others have said, figure out the type of bike you want. That will narrow down the component options. Then figure out price range and you will get it even tighter.
As an example, let's say I figure that I want a road bike. I decide that I want something steel with at least a Shimano Sora group. Figure out what that bikes sell for new. Cut that in half. Here is your target. Now look for steel bikes with that group on ebay and see what they are selling for. See if the "half price" target is accurate and adjust it up or down. Now see if you can find this steel Sora bike. You probably can't. You might find a bike with some Sora parts and some "other" parts. Figure out how those other parts compare to Sora and adjust your price up or down. Perhaps the group is a different manufacturer, figure out where those parts compare to your parts. It is literally going to be this tedious. At first. After a while, as I said, you will start to recognize things and you'll need to research less.
As you go along, you are going to miss out on some great deals. Hopefully you also miss out on some things that would have been a mistake! Your judgment will sharpen.
NEVER BUY A BIKE WITHOUT RIDING IT unless you are willing to deal with some potentially large problems that require things like new wheels or new bottom bracket/cranks or new shifters, etc. Sometimes sellers do not even know these problems exist because they ride on destroyed hardware completely oblivious to the problems.
Oh yeah - keep in mind that quality tires could cost $100 so add or subtract accordingly.
