I'd assume that New Jersey Transit will run all MidTown Direct trains via Hoboken tomorrow, allowing the ALP-44 and ALP-46 engines that these trains normally use to be placed on Coast Line and Corridor trains to help replace some of the engines that are stranded in Sunnyside/Penn Station (routing MidTown through Hoboken would allow NJT to use Arrows). I'd assume Coast Line and Corridor trains will terminate at Newark/Penn, but I could see some of them using the Waterfront Connection to continue on to Hoboken.
Don't know about Amtrak, I'd assume they would terminate at Newark. Either way, Penn Station should be a lot quieter tomorrow, with only LIRR trains and a few Amtrak trains (Boston runs, northern half of Vermonter, Lake Shore Limited, Empire Service, etc.) trains running.
UPDATE (Edit): NJ Transit is stating on their website (http://www.njtransit.com) that there will be limited service between NWK and NYP on Friday. My guess is that this will be limited to select Amtrak Corridor trains and select commuter trains...I'd still guess that MidTown is going to Hoboken, and many trains will terminate in NWK.
[Edited 2005-05-13 06:07:22]