I agree totally with Exodus, WinUAE has gotten worse and worse ever since Brian King took over development. As was noted, it's mainly the Windoze-specific parts that are buggy, these are the bits Brian is responsible for. :-(
I use WinUAE 0.8.8R9, it's the best version yet. If anyone wants me to post this, just yell. But I would not say that ANY version of WinUAE is stable, they are all quite prone to crash at any time for no reason, even when you are not doing anything with it.
JIT doesn't work at all on my machine, and trying to load a saved state results in an instant crash. So the two main "improvements" since 0.8.8 don't work. The only decent thing to happen in the last few years has been 68040 emulation.