Don't worry about it. Nobody going there to live is having problems with visas. Living in Asia is very fluid. You don't have problems there. You simply plan A, plan B, etc. If plan A gets blocked, then you happily go with plan B while you work out plan A. Or maybe you go with plan C just for kicks. No matter what happens, you don't sweat much of anything. That's Asia. (I'm in the Philippines)
Are you also American, but living in the Philippines? How do you like it? Why there?
You can keep re-entering the country as a tourist and get an extension from what I've seen. There are a lot of places that do visa runs over the various borders. I would advise being very mindful of visa issues and respecting the laws. It's very easy to get around and get visas, but don't play around with the expiry. If you do plan to stay longer term, figure out a proper visa.
To be more specific on my advice, if you are mobile then you have a wide area to chose from. Thai visa is a pain? Then try Cambodia, Laos, Vietnam or the Philippines. There are so many places to see here that you don't have to worry much about where to stay. Keep your plans flexible and be open to different routes.
That said, you won't have a problem with Thailand. I haven't had to deal with the 90 day visa limit there, but I'm pretty sure that it's an easy visa run to stay on for another 90 days. Living in Asia, that's too much of a pain for me though, which is why I chose the Philippines.
The good: You can live a pretty good life for quite cheaply. Depending on where you are, I found the Internet connections to be decent, the food to be tasty and the people kind. If you stay there long-term it is important to pick up some of the language as it will bring you closer to the locals. You may also find that you are able to get better prices as a result.
You can do border runs quite easily (Cambodia, Myanmar, or Malaysia). There is an entire industry that has developed around this purpose. When I was there, the visa terms were different depending on if you flew into the country or if you went over a land crossing. I would check out the latest situation on WikiTravel or the Lonely Planet forums.
I personally met another American who over-stayed his visa by over a month. Believe me, you do NOT want to be that guy. He had a horror story about the situation, and ended up having to pay a hefty fine.
Feel free to reach out to me if you want more details.
Staying in Thailand for less than a year at a time is easy to do. If you want to stay on a more permanent basis you'll need to either get married (marriage visa), enroll in a Thai language school (education visa), or be over 65 and have 25 grand or so in the bank (retirement visa).
If you can wrangle something, it's a wonderful place to live. There are the well-known sights and the low cost of living, but for me it goes much deeper. I've become a calmer and more thoughtful person, quicker to smile and slower to anger just by spending two years among the Thai people.
Re: gexla's post – he makes it sound a little cavalier, but there really is a sense in Asia of "eventually this will work out somehow". There are limits and boundaries where this doesn't apply, of course, but in general I find the saying about India applies equally well to Thailand: "everything will be all right in the end. If it's not all right, it isn't the end" ;)