By checking in online (within 24 hours prior to your flight) with Airtran, you can skip going to the ticket counter once in the airport if you have no checked luggage (or use curbside luggage check-in if your airport offers it). We do this so we can just go straight to security & the gate. Also, if you didn't pay for your seats ahead of time, you can choose your seats at this point, from what's left.
I have no idea on the car rental check-in!