For the most part, I recommend you stick with Garuda. (Unless your travels are taking you somewhere obscure that Garuda simply does not fly.) There have been a lot of smaller carriers that have sprung up over the past few years. Some of them, such as Adam Air, seem to be OK, while others are a little more sketchy. (My favorite airline motto is for Wings Air: "We Fly Cheap" - even painted on the planes!)

While Garuda's domestic service is nothing fancy, it is probably marginally more reliable than its cheaper competitors, and it has the largest route system of any of the carriers. As some other people have noted, you are probably best off buying your tickets in country, as they are cheaper and you will be getting a paper ticket (no E-tickets yet!) issued inside the country. Even the shortest flights seem to have a snack or a meal of some sort (as well as the ubiquitous hard candy). And if you go to Bali, stay at the Intercon!