I've just spent a week looking at this with my g/f lately. We're planning to go for 2 months.
We are going to spend some time in Bangkok and a little on the beach, maybe Surat Thani, as well. We want to spend a lot of our time in the central and north part of the country. A week in Chang Mai and then a few jungle / nature treks around that area. Some of the hotels I've seen pictures of in Chang Mai are amazing and only $29 USD a night.
I'm trying to set a few days aside so I can go puffer hunting in the Mekong, that's still under negotiation. We were thinking that one of cruises down part of the Mekong would be pretty neat too.
Here's some pretty good links I've found.
http://www.mautour.com/index.html
http://www.thaitourism.com/index.asp