Although the most important difference hasn't even been mentioned yet - Jogl's reliability is terrible compared to LWJGL, even more so when you attempt to do fullscreen.
I can backup Markus' statement (who didn't agree to the above).
For my JOGL game project I've no real problems with window or fullscreen mode, aside the usual "ATI's OpenGL driver can cause many more problems than Nvidia's"...
I've had no problems with Nvidia graphic cards so far but a few with Ati's. However the many workarounds in JOGL for exactly these ATI bugs solve the current issued. Of course you never know which bugs ATI's going to "implement" in a future Catalyst, but Ken tends to react fast.
My game isn't a Swing GUI'ed JOGL app. Maybe Orangy's is? I only use a few Swing components laying next to the JOGL GLcanvas and these work with no problems.
Speaking for my game project (which isn't finished yet), JOGL's reliability isn't terrible but actually very good.