The following issue occurs when Projects and/or Files windows are undocked (i.e. dragged out of the main window) and doesn't occur otherwise:
Whenever I select a file that is not currently open and press Enter or double-click it, the file is opened in the main window, but the main window doesn't gain focus. If the file is already open in the main window, it does gain focus (so there's no problem in this case).
The problem occurs for all mimetypes I tried (java, plaintext, html, xml), except, weirdly, for .properties files, which do focus the main window.
Product Version: NetBeans IDE 6.8 (Build 200912041610)
Java: 1.6.0_16; Java HotSpot(TM) 64-Bit Server VM 14.2-b01
System: Linux version 2.6.31-17-generic running on amd64; UTF-8; en_US (nb)
Ubuntu 9.10, KDE4
Seems to be fixed in 6.9 RC1. Will test more and report back.