Practically everywhere is in the lonely planet/rough guide. Pai and Nan are both pretty well covered. If you go to Cambodia or Vietnam, fixing transport to get anywhere else can be tricky.
Don't think that Thai islands, in particular, are "undiscovered" because they're not in the guides - quite a few have been developed as exclusive resorts.
Also, think about visas. Thailand has the most complicated system: if you're a UK citizen Thailand will let you in for one month without a visa, two months with one. There is no way to extend either; you have to leave Thailand for a bit. Technically you need to have proof of transport out of Thailand if you arrive without a visa; they didn't check mine at Suvarnabhumi but they did at Chiang Khong up north.
In your shoes I might spend a month island hopping in southern Thailand; fly to Cambodia or Laos for a month (both countries issue 30-day visas on arrival for virtually everyone); and come back to Chiang Mai and the northern Thai hills for the last month.
I wouldn't advise trying to fit a lot more in three months, to be honest. If you go to Vietnam, skip the South and spend longer on Cat Ba island in the stunning Halong Bay (like the famous islands around Phuket, but more extreme), and in the mountains around Sapa (like the famous mountains around Chiang Mai, but more extreme!)
Don't think that Thai islands, in particular, are "undiscovered" because they're not in the guides - quite a few have been developed as exclusive resorts.
Also, think about visas. Thailand has the most complicated system: if you're a UK citizen Thailand will let you in for one month without a visa, two months with one. There is no way to extend either; you have to leave Thailand for a bit. Technically you need to have proof of transport out of Thailand if you arrive without a visa; they didn't check mine at Suvarnabhumi but they did at Chiang Khong up north.
In your shoes I might spend a month island hopping in southern Thailand; fly to Cambodia or Laos for a month (both countries issue 30-day visas on arrival for virtually everyone); and come back to Chiang Mai and the northern Thai hills for the last month.
I wouldn't advise trying to fit a lot more in three months, to be honest. If you go to Vietnam, skip the South and spend longer on Cat Ba island in the stunning Halong Bay (like the famous islands around Phuket, but more extreme), and in the mountains around Sapa (like the famous mountains around Chiang Mai, but more extreme!)