Sound like one or more of the databases were damaged during the crash.
Stop the filemaker server (if the java GUI doesn't respond, you can use the command line, http://www.filemaker.com/support/product/docs/12/fms/fms12_help.pdf )
Open each database directly from a filemaker client using File->Recover. This will scan the database, fix any issues, and save the repaired copy as a new file.
It might tell you that you can't trust the file going forward, and you'll need to use an uncorrupted back-up copy (from before the crash)--empty it of data and then import the latest data from your recovered copy.
In any case, the recovery process generates a big log file that you can scan through to see where any problem lie (hint: any line that doesn't have an error code of 0).
It's a bit of a pain, and can take a couple of hours (depending on the size of your dataabses) but users are usually understanding if they can see you are working towards a solution.
It could also be that that Server is running a consistency check on each do to the uncontrolled close of the files. With gigabyte sized files, it can take a long time for just one such file to complete a consistency check. You may find that after a long wait, the files go ahead and either open or report damage to the file.
> It could also be that that Server is running a consistency check on each do to the uncontrolled close of the files.
This is true—server-side consistency checks seem to take forever and a day compared to their client-side equivalents.