Approximately once a week we get someone asking this type of question on OTN.
Usually it is something like "I can't get the log window to show up even when I go to the view menu" you can replace the log window in this post with any of the other windows inside JDeveloper.
Usually it happens when someone was messing with the windows and moving/resizing/collapsing them too much and some how minimized them to a size 0.
The solution for this problem is to rename/delete the windowinglayout.xml file from the jdevsystemoracle.ide.10.1.3.39.84 directory.
This returns all the windows to their default locations.
As a side note specifically for the log window I usually have it minimized - it pops up when something is being written to it. And don't forget that when you want to get a look at this long stack trace your class just dumped you can double click the log window's tab to maximize it to it's full size and save you the scrolling time.