I'm sure that there are plenty of methods used by folks but one thing that I do is when I do find a common ancestor, I will graft that person's line into my own tree because there may be times when someone else who matches me will have their connection through one of the same people in that other line. It is also important to investigate the collateral lines from those people too. People wonder how I have over 30k people in my tree and that's one reason.

Also, when I start to see a lot of the same surname in my matches' trees but don't know how I am connected to that particular family, I will start researching that family by looking for books online and then seeing whether any of the branches from that family shared a common geographic area with my known ancestral families. Ancestry.com has a lot of books available through a card catalog plus there are a lot of books available for viewing on the FamilySearch.org website.

Whatever works!