2000-06-03 80:23:11,220 ERROR [Naming] Could not start on port 1099
java.net.BindException: Address already in use: JVM_Bind
After a quick check with Active Ports i saw that iTunesHelper.exe held the port. And when the process got killed, Eclipse started working as expected again. 1099 might have been assigned to iTunesHelper since it's inside Windows' ephemeral port range. Just to be sure this doesn't happens again I removed the auto start of iTunesHelper from the registry.
And adjusted Windows' ephemeral port range so that some other service doesn't grab the port. There's a great guide over at ncftp.com on how you do this for different operating systems.