What's the difference between Android 2.2 Froyo and Android v1.6 Donut?
There are HUGE differences between 1.6 and 2.2. 1.6 is also a pretty old version of android. Flash is only available for 2.2 and later, so if you have to have flash then you need to go with 2.2. But the archos 43 does not have an FM receiver, the 48 has a receiver, and transmitter. 

The UI had big improvements in 2.2 compared to 1.6. The ability to install apps on an external sdcard is also available on 2.2, but I don't think you will really need that as the 48 says it has 500GB (that seems like a lot for a device like that...). I have also read that it is possible to install froyo on the 48. 

3.x is currently only available on select devices as they have to "partner" with google in order to have access to Honeycomb (3.x). So I wouldn't expect to see an update on these devcies anytime soon for 3.x.