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 very few people speak English (but nowadays, more and more people actually do), everyone wants to take a photo of you, and that arranging sightseeing activities may require more legwork than other destinations.
Flights land in Sentani airport, Jayapura, about 60km from downtown. There are direct flight (with stopovers, but no change of aircraft) from Jakarta, Bali, Makassar, Ambon and within Papua - most bigger towns including Timika, Sorong, Manokwari etc. Most Indonesian airlines fly to Sentani, including Garuda, Sriwijaya, Lion air etc.
Taxis are IDR250,000 as of April 2014. There is an airport bus, called Damli, which departs at irregular times and costs 50,000 per person (July 2014), no matter how far you are going. It has plenty of space for luggage.
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 (PGK10, 50min). Once across the Indonesian border there are taxis into Jayapura (IDR200,000 per person, 2h). (NOTE: The land border was closed in April 2014 after some shooting incidents and crossing was only possible by boat, which is more expensive. Immigration formalities were then moved to the harbour in Jayapura. In July 2014, the border was expected to be opened up again. Please check before traveling!).
A travel permit ("surat jalan") is not required for Jayapura. However, it is easy to obtain a travel permit from Jayapura Police Station if you want to travel to some other places in Papua. The police station (Polda Papua) is located on the main street across Jayapura Mall. The office is open every day including weekends and bank holidays. It takes about 20 minutes to get the travel permit issued. It should be issued at no cost, but some travellers report having been "charged". You need two passport photos and your passport (or a copy of its picture page), the Indonesian visa page and the stamped Indonesian departure card. They might able to make copies for you. You need to mention exactly all places you are planning to visit in Papua, including places close to Jayapura (for example you need a surat jalan to visit the memorial). Once you get the surat jalan, make many copies of it - you need to show it at any police station and leave a copy there.
The public transport system consists of numerous minivans (bemos, also locally called angkot or "taxi", although there are taxis in the more traditional sense of the word) which have their destination route printed on the side. Each trip usually costs IDR3-5,000 per person, depending on the time of day, the distance the bemo is going (not the distance you are traveling) and the driver's mood. Ask before, or just ask the other passengers. Jayapura's outskirts (other towns actually) follow the road west of Jayapura to Sentani (where the airport is) and beyond. Few (if any) bemos go all the way between Jayapura and Sentani. You normally change at dedicated terminals, if you have to go longer distances. West of Jayapura these terminals are (in order): Entrop, Abepura, Expo, Sentani. See the Get In section for getting between Jayapura and the airport using bemos.
Dedicated drivers can be arranged through the Bel-Swiss hotel for around IDR600,000 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. You need a surat jalan to visit.
Hamadi Beach is a local harbour 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 (IDR20,000). 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.
Danau (Lake) Sentani is outside Jayapura city itself (30min). It is a large freshwater lake surrounded by steep mountains. A small number of restaurants and guest houses are located on the edge of the lake.
Between Abepura and Entrop the main road winds up and down the side of the hill from where the views over the bay are great. There are two places that have a few tables and sell coconuts (from 10,000). This is a great place to enjoy the view and mingle, but bring mosquito repellent.
A number of local craft stores in Hamadi sell Papuan wood carvings, bark paintings, and other artefacts.
Abepura markets are a large local market in Abepura (20min 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 IDR40,000.
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 (5min drive from the city), however, they are not heavily frequented. The Swiss Belhotel bar is nice but quiet.
The Swiss-Belhotel provides international four star accommodation for around IDR650,000 per night. The facilities are high standard and the pool overlooks Jayapura harbour. Importantly for travellers with no Bahasa language skills some of the front desk staff can speak English.
A number of other (and cheaper) hotels are located in the city.
Telkomsel has good coverage in the area for calls and mobile internet.
There is a friendly Papua New Guinea consulate that issues visas for 5 working days, free of charge. You can leave your passport at the consulate and travel to other parts of Papua with your surat jalan, while waiting for the visa application to be processed.. Someone else can pick up the passport for you, if you fill out the confirmation paper you receive once you hand in your application. The PNG border can be crossed by boat or overland (see the Get In section).
Flights to Wamena in the Baliem Valley cost 925,000 rp one way with Trigana Air. There are up to five daily flights and getting a ticket the day before should not be a problem, unless it is festival time or other busy times.
Pelni has ships going to other parts of Indonesia.