i've asked this a while back, and there isn't a plugin pack because there are many legal issues you would have do deal with plus there would be so many updates that would make it a big hassle.
yes, the really unfortunate thing is that (partially due to the zilmar plugin spec), you can't even FIND all the plugins and have an emulator seemlessly choose between them, depending on what will work for each rom. How sweet would THAT be?!?
Can PJ64 be run from a command line type interface like ePSXe?
ePSXe has ePSXecuter (Pete Bernadete strikes!) which seems to manage everything QUITE nicely.
Afaik, there are some command-lines. One that i know of is that if you start pj with the command-line pointing to a game, it will begin emulating this directly.
It is like that the "GUI" of pj does. That's why it closes before the game starts to emulate...