I had some experimenting running bochs and I found some answers during my try and fails.

I did manage to install a SVGA driver and I could change the resolution up to 800x600. But it was still in 16 colours. Might have gotten more colours if I tried some more, but it takes time to make changes, restart, get error messages and so on...

The mouse capture toggle was easier than I thought, just use the middle mouse button for that:)

I did not succed in getting .iso files to work as CD's in Bochs. So I installed MacBochs, but had trouble getting the cd's woring there as well. Next I ran Bochs on a windows machine, and then I managed to use the CD's.
Tried installing Win2000, but it always freeze when starting up the first time. Also tried DSL (damn small linux) and Slax, but both will hang during booting the Live CD. There may be some console options around these issues though.
Then I installed Win98SE, this was sucessfull.

So copying the diskimage file to MorhOS and it runs. A bit slower than win95 though.
By default the clock is not synced at all under bochs. This makes the clock go much faster than it should, as well as the timing for everything. Eg. the animation when copying files goes real fast. I think this drains cpu power as well. I noticed that whatever I set the IPS to (how fast machine you want to emulate), the CPU usage on MorphOS was close to 99% all the time.
I had IPS set to 1000000, and set the clock to slowdown mode. Then the CPU usage got around 40% at average, but sometimes short peeks up to 90%. However this also affects the emulation speed, it felt more jerky. So setting the IPS to 3000000 improves this, but now the CPU usage is back to almost full again. But I think it is slightly faster like this. And at least the clock is running in normal speed.

For comparisation I would say that the MorphOS version runs quite well. It ran fastest on windows, but this was on a 3.4Ghz P4, so that was no surprise. And since the clock was not synced at that time, the clock ran so fast that a double-click was impossible inside the emulation.
On MacOSX it runs at similar speed as on MorphOS, this is expected since its the same hardware. But the mouse capture did not work properly, the Mac mouse was still present and was moving faster than the emulated one. So it was very annoying to use, had to disable the mouse and get a new capture to reset the position. A nice feature on MorphOS and OSX is that you can mount the harddisk files and read/write files to the emulated disk. On windows I'm not sure if the diskimages can be mounted out of the box. One other benefit I think that MorphOS have over OSX is memory usage. The OS uses less memory, so you are able to select more memory for your virtual machine.
All tested versions was 2.1.1