the absolte cheapest way are the government buses, these are abit of a gamble...but a experence none the less. i used these around 3 or 4 times over there..one time was fine - empty bus and direct, another was only a small trip (2hr cab ride) ended up taking all day on one, i was the only white guy and it stopped all along the way as if it was a suburbian bus, got very full with people standing for ages. but they are very cheap. didnt make it on a train at all, but they seem around the same deal as VIP buses, which are normally direct and air-con (mind u all the government buses i went on were aircon as well)
as with flying, it might not be out of your budget after all if your going in the off-season, i just had a look while doing some research for my next trip and it seems u can fly almost anywhere around thailand/sea for no more than 50usd on www.airasia.com
worth a thought for some legs of your jouney espically if you were considering vip buses or trains...they may cost up to 30usd for long legs anyway...