International travel to Jayapura is almost non-existent and as such you are unlikely to meet other tourists. But many missionaries from around the world actually work here. This seems to mean that tourist touts are rare and beggars are not in the city. Furthermore, the closest thing a market stall holder will do to have you look at their goods is smile.
On the other hand, it also means that a small though increasing number of people speak English, everyone wants to take a photo of you, and that arranging sightseeing activities may require more legwork that other destinations.
Flights from Jakarta land in Sentani airport, Jayapura, about 60 KM from downtown.
Overland from Papua New Guinea takes around 3 hours drive from Vanimo. For visitors coming from PNG an Indonesian visa can be arranged at the consulate in either Port Moresby or Vanimo. Public Motor Vehicles travel regularly between Vanimo and the Wutung border crossing (K10 / 50 mins). Once across the Indonesian border there are taxis into Jayapura (RP 200,000 per person / 2 Hours).
The public transport system consists of numerous minivans which have their destination route printed on the side. Each trip usually costs RP 2000 per person.
Dedicated drivers can be arranged through the Bel-Swiss hotel for around RP 600,000 per day.
The General MacArthur memorial is set on a hill overlooking Jayapura harbor and city. Whilst the memorial itself is basic, the steepness of the terrain makes the site a spectacular vantage point. A number of old Dutch colonial houses can also be seen on the road up to the memorial.
Hamadi Beach is a local harbor beach near the city. On the beach are four large artillery embankments from the second world war. Further down the beach are the local fish markets. The beach itself is not very well kept and covered in rubbish. However, at night a number of food stalls are set up and provides plenty of atmosphere.
White sands beach is an ocean beach a small drive out of the city. This beach is owned by local Papuans who charge a small entry fee (RP 20,000). In return for the fee they keep the beach clean of rubbish provide basic toilet facilities and shaded areas to sit. It is a picturesque beach with soft white sand and well worth a visit.
The area around the governors residence consists of old Dutch colonial villas, some of which still have what look to be traditional style gardens.
Lake Sentani is outside Jayapura city itself (30 mins). It is a large freshwater lake surrounded by steep mountains. A small number of restaurants and guesthouses are located on the edge of the lake.
A number of local craft stores in Hamadi sell Papuan wood carvings, bark paintings, and other artifacts.
Abepura markets are a large local market in Abepura (20 mins drive from Jayapura city). This market caters to locals and as such does not stock tourist items.
Jayapura city markets seem to be open every night and sell a broad range of items. Although most are for local consumption cheap clothes, accessories, DVDs etc. can be found here. Local produce is also sold at these markets and makes for an interesting walk.
The street food is plentiful and good. Different areas of the city have their own specialty. On the road from the Swiss Belhotel to the city are BBQ seafood stalls. The eastern most main street of the city has a large number of satay chicken stalls (although satay stalls are pretty much everywhere) and on one of the cross roads between the two main streets are noodle soup vendors.
The most expensive street food will costs you less than RP 40,000.
Drinking in Jayapura is limited. Most restaurants will serve Bintang beer if you ask; however, these may not necessarily be cold. There are some bars and nightclubs in Entrop (5 mins drive from the city), but they are not heavily frequented. The Swiss Belhotel bar is nice but quiet.
The Swiss-Belhotel  provides international four-star accommodation for around rp 650,000 per night. The facilities are at a high standard and the pool overlooks Jayapura harbor. Importantly for travelers with no Indonesian language skills, some of the front desk staff can speak English.
A number of other (and cheaper) hotels are located in the city.