Can't help you with Wonosobo. Ask Mas Fred about that since he used to live there.
For Jogja, I have stayed at Ibis hotel last year. It is right on the main street of Malioboro. Clean, friendly, priced fairly well, central location.
Just remember to bring a hat and suncream because it is bloody hot in Jogja.
Oh, you can also look up;
www.yogyes.com - hope I don't get an infraction for that one ;-)