Bob's advice is very good.
When checking baggage I generally designate my pick-up time as a half hour after the airline's expected arrival time for rental companies that are at the airport and 45-60 minutes for off-site companies.
In addition to the first level safeguard of including your flight information when you're renting, it's always a good idea to call the rental company if you know that you're being delayed so that you can be assured of having a vehicle when you eventually get to your destination.
Finally, if you haven't already I'd suggest that you join the frequent renter program of your car rental company - most of them are free and you can join others', like National's, without a charge by going through the special deal that mousesavers.com makes available - so you can save time when you rent by skipping the 'regular' renters line. Even if you will never rent again that one tip will get you on your way to your vacation, where you'll wait in other lines but they'll be more fun. If you've already made your reservation with a frequent renter program number you can call the company and have it added when you get one.
Dick Taylor