There's a flight search tool I just discovered from one of the many Japan planning sites I've gotten lost in since I started working on planning our first Asian adventure, and it is incredible for figuring out multi-city itineraries. We're in the Detroit area and just searching Kayak or Delta gives me $2K+ pp r/t if I go Detroit to Tokyo to Hong Kong to Detroit (or switch the two destinations), but this site found it for about the same price as Detroit to Tokyo without the detour. It takes some playing around with, but it is so much better than any other airfare search tool I've ever used that it is well worth it!
http://matrix.itasoftware.com