1. There is now a new Quick Search box at the upper right corner, with shortcut key
Ctrl-I. The pull-down list shows it can search for Types, Actions, Options and help items. It seems interesting and I should use it more often.I usually use Ctrl-O to jump to a class in my projects, which is very fast. Or use Alt-Shift-O to go to a file (much slower than Ctrl-O). In NetBeans 6.1, Ctrl-O (go to type) used to show all the useless javascript files except the java classes I was looking for. Now 6.5 seems to have fixed it.
2. Refactoring is extremely slow. Any refactoring, even renaming a local variable is slow. The blue progress bar stops at 100% for close to 1 minute in my computer. NetBeans seems to be searching across all projects and cache and gathering dependency.
3. Sometimes at startup, it shows a background task "Transfering Repository Index :Central Repository" (NetBeans typo: it should be Transferring). It's not blocking anything but does take quite long to complete.