I flew from DJJ to Vanimo in '97 (I think) in a PX F28. Took about 15 minutes.
I get to both Vanimo & Jayapura a few times a year and have seen the odd aircraft do the crossing. Bob Bates' P2-BOB in Vanimo a while ago on its way to/from Papua and a few Indonesian MAF types there more recently as well. Sight seeing from what I can gather.
Airlink did a once weekly flight from POM (via Daru?) to Merauke for a while.
There has also been a few reports of Indonesian military aircraft flying low over Vanimo & Aitape. Hercs I believe. Of course nothing official...
Not a huge amount of traffic. The land crossing is quite well organised now. The road from Vanimo is very scenic.