Hi Boothee,
Depending on whether you are doing filtered exposures (AVI capture) or single shot imaging, and also how much you time you need to take to change filters for the first approach. In my experience through filtered exposures, each AVI per primary colour channel takes about 35seconds optimal for my current system (8" F31). I have tried 40 seconds which is what others have adviced but found it to yield considerable field rotation, added to the fact that the manual filter wheel has to be rotated for each colour channel. The time taken for wheel rotation takes up around 2-3 seconds, so i figured it would be better to restrict AVI exposure per channel to about 35 seconds (and again, I would stress for my system). Depending on the effective focal ratio of your system, the exposure duration varies slightly. More importantly, as long as you can obtain at least 1000 frames cumulative per colour channel, it would be a good enough basis for reduction selection under Registax.
Now, the picture changes if you are using a single shot colour camera (Toucam, etc), since there is no need to take time to change filters, you can expose Jupiter longer. As JY has mentioned, 90 seconds is a good rule of thumb, but it is worth exploring based on your system. I have a formula worked out on my website article (accessible from
www.celestialportraits.com) to derive the recommended exposure duration for single shot cameras.
Do take note that out of a certain N number of frames gathered from an AVI, it is best to take M number of frames (M<N) from this set based on the Gradient selection alignment method in Registax. Also, it is better to have a few very good frames for stacking rather than to stack everything together in large numbers. You will very often retain critical surface details better thereafter.