Well -- this is one of those "it all depends" things. Getting a low rate on a car rental is almost an art form. First of all, start with a site such as Kayak in order to get a "general" idea of rates and possibilities. Narrow your search down using specific tools, such as Costco.com and partner websites you might have affiliations with, such as Southwest. There really is no "best" rental company, it all depends on what deals are available at the time. For example, most of my rentals locally for business are with Alamo. Late in October my wife and I are going to Charleston SC for a gathering and the best deal ended up with Avis through Costco. Next April we're going to Maui for a vacation for a couple of weeks, and the best deal was with Alamo (via Costco). My local rentals are not through Costco, but usually through Southwest using a combination of the Southwest RR code and a Visa code that provides an additional $30 discount. Alternatively, if you don't want to do all the research and labor yourself, you can use sites such as autoslash.com and see what they come up with.

There is NO, I repeat NO value in allegiance to one rental company over another, with one exception: I'd suggest sticking with the majors and avoid the small players. The problems with the big players (e.g. Avis, Hertz, Alamo, Enterprise, yadda yadda) are bad enough without compounding things with a small player with a funky attitude and weird rules.

Hope this was helpful.