Does anyone have a good reference or site for Scots surnames and septs?
The two main references that I'm aware of are Black's "The Surnames of Scotland" (1946) and Collins' "Scottish Clans and Family Encyclopedia" (1998). I don't believe either is freely available in digital form but you can find them in libraries or there is a searchable snippet view of Black's at http://books.google.com/books?id=fQotAAAAMAAJ
Is there enough data yet to show whether y-DNA really correlates with clans? In my case I know it doesn't... the major DNA group in our surname (a subgroup of L193) connects to a Scottish "superfamily" of 5-6 names (Vans, Little, Glendenning, Elliott, McClain) that have a strong Borders connection but no real clan affiliations. Of course the clan system was less strong in the Lowlands anyway.
We did have a small branch of our surname who migrated up to Inverness and became affiliated with Clan Munro, which means the name shows up in Collins and Black associated with Munro. But that branch died out by the 17th century and there was no other Munro association... it doesn't stop some family members from running around the Highland Games today in Munro kilts, but it's not really relevant to the history of L193 or of our surname.
Anyway, the one example certainly doesn't mean clan affiliations don't matter in general, but I've always wondered whether their influence was really strong enough on dependent families outside the main clan name. At some point there should be enough data to analyze y-DNA against the wider clan affiliations for possible correlation, but I don't know if we've reached that point yet.