My overall ranking would be Garuda, Air Asia, Lion, and the rest.

Air Asia is very cheap, has functional online booking, and is quite safe -- AFAIK the entire group does their maintenance in SIN. Being an LCC, you do run the risk of delays, but I've never had any significant problems and esp. early morning flights are usually bang on time.

Lion is Indonesia's 2nd carrier and Garuda's biggest competitor. They have a bunch of nice new 737-900s (and a bunch of aging MD-8xs too), a tolerable safety record and a good network. Seat pitch can be tight though, and delays and cancellations are more common than with Garuda.

The rest are probably best avoided, although Mandala and Batavia have been making some strides towards international acceptability, and I'd still take any Indonesian airline over the average ferry. Merpati -- a parastatal like Garuda, but specializing in smaller aircraft and obscure places -- is particularly notorious for cancelling flights at the drop of a hat.