We don't have a crazy commute for gym, but this year we've started having a long one twice a week for diving with the boys.
We found those organizers that attach to the back of the seat and set them up as homework stations. Pencils, pens, colored pencils, crayons, extra paper, calculator, ruler, anything else they might need. Unless your car has them built-in, don't forget booklights and spare batteries!
We bought Taby trays (I think that's what they're called), so they have stable work surfaces. DH created a removeable cover out of clear plastic so the kids can decorate they trays without damaging them and can change them at will (like a desk pad?).
We found an organizer that fits between their seats (we have an SUV and they like the third row) to store books, workbooks, etc.
We made the same for the girls. Since they sit in the second row, which is two separate seats, we found a stand up car trash can that was big enough to hold any books. It attaches to the floor with Velcro.
I also turned baby wipes containers into "spare time" kits. They have activity books, small games, crayons, and other non-noisy things to help kill extra time.
We use a timer to break up the commute into set segments for each subject and free time as well.
Our car has those headrest screens and a dvd player. DH records programs for the kids to watch only in the car---think those PBS afterschool educational shows. Or, Discovery Channel/History Channel programs that relate to something the kids are interested in or studying. Each kid has color coded headphones at their seat, but I control the DVD player.
I invested in a cooler that charges from the car. We keep it stocked with healthy snacks and drinks, as well as medications and a first aid kit.
In the back end, we have activity bags packed with spare uniforms, gear, first aid equipment, and emergency information for each of our kids. Each kid has a color (blue, red, purple, and pink).
I found drawstring backpacks in each color for the activities. Whenever possible, we buy gear and supplies in the different colors. We also label everything--name, birthdate, phone number, and allergies. The pockets of the duffel bags are filled with the gear and supplies that any of the kids could use.
I used cloth diapers with the kids as babies, so I have a bunch of those ditty bags--oilcloth bags designed to store dirty or wet clothes---on hand.
It takes remembering to keep the bags stocked (and to wash anything that might get stinky) but the system works.
I found one of those portable office organizers and use it in the front seat (or front floorboard if DH is in the car). When I pick up the kids from school, they know they have to immediately hand me their daily folders. I spend five minutes in the parking lot (after moving out of the line of traffic) checking their folders and doling out their afternoon snack--usually cheese and turkey cubes or something else high in protein. We then hit the road, either to home or practice. While they are in their activities, I check their homework, sign important papers, and the like. That way we still have time later to talk about or fix anything.
I find that a schedule is really helpful. Sticking to it can be hard, but once you get used to it, it helps everything run smoothly.
Whew! Sorry for the long winded post.