Consider a tiny restaurant in the centre of Jogja, called Atap. It serves sirloin steaks, fish and chicken (all reasonably priced), along with some interesting beverages, such as "Osama Coffee".
Atap is just up up the same street as Bar Bintang (another of nice stop), that also serves a great selection of food.
There is a great restaurant called Gadjah Wong - it serves fusion Western & Asian cuisine. It is a nice, upscale restaurant located in a quiet neighbourhood, with live 'gamelan' - Indonesian traditional music.
Bale Raos serves "royal food"- the favorite cuisines of the Sultan!
Dixie serves pasta, and a wide variety of beverages (like the Lemon Mint Splash).

