As was mentioned, the "refinery quota" is the number of refineries that can work for a given extractor. If you put a refinery in range of an extractor (in its own gravity well, or one hop away), the refinery increases the extraction rate. You can add up to the quota and get a bonus for each one, past the quota they don't work anymore.
As for how effective refineries are... IMO, they're not worth spamming. You don't build a refinery everywhere. You certainly don't build several refineries everywhere. In a system with only one or two extractors, they're rarely worth it.
But because they also work on neighboring gravity wells, if you have a well that has several others connected to it, building 3 extractors in that one well will apply the bonus to all of them at once. In that case, they can make a real difference. Here's an example, where A B and C are all gravity wells with extractors.
A --- B --- C
In this case, the only place you want to build 3 refineries in B. Those three will cover A, B, and C, hitting the quota for all of them. Build no refineries in A or C.
If you build 1 refinery in each instead, B will hit quota, A and C will only be at 2/3 and you'll get reduced benefit despite spending the same amount to build the refineries.
Hope that helps. 
