it's a set neck that is contoured so that it feels like a neck-thru
Current Gear:
Ibanez rg470
Peavey ValveKing 112
Blackheart little giant head
2 homemade 112 cabinets
Boss SD-1
in terms of ESP or LTD's, set-thru simply means a set neck with a sculpted heel, such that it feels like a neck-thru.

But there are variants of the set-thru which is simply a set neck with a long tennon, extending almost to the end of the guitar.
Peavey 5150, LTD EX400BD, tubescreamer, and a whole lotta fingers