Keep an eye out to see if your rental company has self-serve kiosks. I know that Alamo has them.
I've bypassed a huge, non-moving Alamo line simply by using the kiosks over to the side that absolutely noone was using. I was done and out to the garage in about 4 minutes. (And when people saw me do that, the kiosks were instantly popular. Amazing how people will join a line without thinking, and ignore other options)
Also, if you're using a company with an in-airport counter and there's a huge line and no self-serve kiosks, trying going upstairs and over to the other side of the terminal. Each in-airport car rental company has two counters, one on the A-side and one on the B-side. 99.9% of the time people just go to the counter on the side where their airline's baggage claim is located. But if one side had a large number of planes all arrive at once, you could have a long line on one side of the terminal, but nothing on the other.
So if you're on the A-side, just go back upstairs to Level 3, cross over to the B-side, and go down to Level 1 to check the line on that side. (or vice versa)
-Rob