I would say that Winuae is as compatible (with settings) as any amiga I've ever had. It is as good as the 500 with old software and the 1200 with practically everything.
If you want your scrolling etc. to be perfect it is best to set your refresh rate to the same as the video mode winuae is emulating if you can; otherwise it will not be exact, because the emulation is so tight the hardware running at a different refresh will cause scrolling especially (to some people) to be not perfect.
For example if you are running a pal mode you will want a 50 or 100 or if neither of those work a 75hz. If you use say an 85hz mode scolling won't be perfectly smooth because the emulation will be running at a slightly different rate than the hardware. If you are emulating a ntsc mode 60, 120 or 90 not 70 85 or any other. Anything other than a whole multiple of the mode you are emulating is less than perfect but totally off refresh rates will be most noticable.
btw v-sync and buffering will help this but not eliminate it as much as a refresh match.
This has never been a problem for me but some purists complain about it sometimes.
