Here's a quick process from my efforts in capturing the double transit of Ganymede and Io (according to Stellarium) across Jupiter last night. Thanks to sitting outside for several hours, I even saw a few - what I assumed to be - Orionid meteors.
Technical details: William Optics FLT-132 on NEQ6, 5x TeleVue PowerMate, Canon 5DmkII, EOS Camera Movie Record in 5x crop mode at ISO 800 and 1/30 sec, best 10% of ~ 3000 frames stacked in RegiStax
As luck would have it, my quick and dirty polar alignment using a compass and the NEQ6's bubble level ended up being remarkably accurate... only a gentle nudge was needed every half an hour at minimum speed to keep Jupiter within the 5x crop mode field of view.
I recorded the entire transit (minus eos_movrec crashes, flat battery, etc) from before 10 pm until just after 3 am (33 GB of MJPEG AVIs). Hopefully I'll be able to assemble a nice animation out of it
Edit: Io is actually on the other side of the shadow... I forgot to update the line when I flipped the image.