I'd have to suggest Wat Phu Tok in the far north-east. It isn't easy to get to, or wasn't 20 years ago, but not only is it a very curious place, it's in a part of the country less influenced by modern tourism. Great fun.
http://www.bangkoklive.co.cc/forums/showthread.php?4809-Wat-Phu-Tok-Thailand about 6 years ago
In my opinion, best would be to base yourself out of Pai in northern Thailand (north of Chiang Mai), or even head up as far as Chiang Rai. The countryside is rolling hills and valleys, with lots of hill tribe villages to visit, and there are many companies offering organized treks of especially out of Pai.
Plus you can combine with other adventurous activities nearby - raftting, canopy top tours etc. about 6 years ago