Bali's accommodation ranges from $10 guesthouses in Ubud's rice terraces to $500/night private villa pools in Seminyak and Canggu. Ubud is the cultural heart; Seminyak and Canggu suit beach and cafe culture; Kuta is budget backpacker territory. Nusa Penida and the Gilis offer quieter island alternatives.
Yogyakarta has excellent mid-range hotels near Malioboro Street. Jakarta caters primarily to business travelers. For Komodo, liveaboard boats are the best way to explore — they double as accommodation and transport.