Ende Airport is located quite centrally, and offers flights on regional carriers to Kupang, Labuan Bajo, Bali (by means of Labuan Bajo) and other destinations. Carriers include Garuda, Wings and TransNusa. Check with an agent for schedules, as they're nothing if not fluid in this part of the world. In high season book these flights as early as possible.
You're encouraged to arrive a somewhat over-cautious two hours before your flight to check in at this tiny regional airport. Once you go through security, there's nowhere to buy food or snacks in the aggressively air-con waiting lounge -- plan accordingly.
Air Wings (Lion Air)
Semi-comfortable air-con minibuses depart regularly for Bajawa, Maumere, Moni and other points further afield, usually in the morning. Your hotel or an agent can help sort out tickets for you. The ride from Ruteng to Ende takes about seven to eight hours depending on the roads.
Inquire at your hotel or an agent for specifics, as things do change regularly. At the time of writing there were regular ferry departures to Sumba (Saturday 08:00) and Kupang (Monday 08:00). A Pelni ferry which runs to Kupang, Sumba and onwards, eventually to Surabaya, passes through once every two weeks. See the Pelni website for details.
Car hire to Kelimutu and surroundings can be arranged by travel agents for around 600,000 rupiah a day. Travel agents can also help you rent a motorbike, a good option for sprawling Ende.
Ojeks are somewhat common in town, although they do dry up at night. Expect to pay around 5,000 rupiah for most destinations around town. The same goes for bemos, which often congregate at Jalan Hatta, located near the soccer field.