mrstein,
I've been diving in Thailand for a while, maybe 10 years 2-3 times a year.
IMHO without question the best sites are in the Similan Islands. Normally these dives are with a live-aboard company, no one lives on the islands. There are many that provide that service. It is also possible to do a day trip from Patong Beach. Its a long day, up early and a taxi ride to the port then a speed boat out to a live-aboard where you dive for the day (two dives), then the reverse back to Phuket, back for late dinner.
Most of my dives have been on Phi Phi. I normally dive with the gang at the Phi Phi Princess resort. Sad to say that the entire resort was washed away. They plan on reopening in December '06. However the owner of the resort, Charlie, had just opened another site a little further south on Koh Mok. Its not as "finished" as the Princess or Charlie resorts on Phi Phi were but its very nice. The famous dive site there is the Emerald Cave, very nice. Also have the odd chance to see a Whale Shark. Check their web site its www.princessdivers.com if you go tell Chay, manager, Dennis said hello.
Not all dive operators on Phi Phi were wiped out. As an example the Holiday Inn resort and the Phi Phi Natural resort on the North end of the island are all fine and operating, as I understand, at normal conditions.
On the Gulf side there are many dive sites available to you. Again IMHO none of which are worth traveling to LOS for just the diving. There are some nice sites off Koh Samui, one of the most famous being Sail Rock. Let me tell you, its a real hit or miss. Unless a boat has already been out there and radiod back to the other boats you have no idea about visability. On a good day its 30+ meters on a bad day its 3 meters. I've hit both. If you get there and its bad, its a real waste of a day.
You can always get trips from Pattaya or the nearby islands, just don't expect anything to special.
Feel free to PM me if you have any additional questions about specific dive operators.