You'll be happier with Fedora - but to be honest your best bet in GEMPAKland is Centos. Especially if you want to use the followon software in 2011, as it'll be written specifically for Centos. Either way - either of those are better than cygwin.
AWIPS II will be opensource. I'll do the same thing that I've done with GEMPAK by offering systems including the software and all the data ingest scripts ready-to-run. Either standalone with Linux or a VMWare file that can be used in Windows / MAC / etc.
Yes; I ran it for a while on my 64bit workstation with no major issues, but have since moved it over to a different workstation with a 32 bit setup (mostly just due to keeping my setup more usable for all the stuff I do).
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