I haven't researched this topic in much detail yet, but I do have a few points:
- Make sure it's really a squirrel problem. Nuts or acorns on your engine are a pretty good sign. Since squirrels are active during the day, you can actually watch for them.
- Squirrels invade cars because they are looking for a dark, sheltered place free from predators.
- As for other pests, deny them food, access, and shelter. Park away from trees. Are they coming because you are feeding birds, and food is available?
Make sure there's no stale beer around that's attracting squirrels, like this one at the student union, Univ. of Wisconsin. Drunk squirrels do the most damage. (Photo copyright by Ambience Photography)
On the squirrel blog, many people talk about using mothballs, cayenne pepper, or other "better living through chemistry." See my post below for mice. I doubt if any of these "magic bullets" work well. These bad ideas are promoted by people who have a product to sell. Instead, think about what is attracting squirrels to the area of your car, and then eliminate that.
Here's a source for all things about squirrel control. I'd be very skeptical about the repellents. Denying squirrels food is a much better idea.
The real solution is just taking the time and the patience to figure out why they like your car or yard (food?), where they are coming from, and how they are getting into it.