You do not say which version of SQL Developer this issue involves or anything about your environment. Perhaps this old forum thread can be of help. Note the comment regarding JDK version -- but that all depends on the SQL Developer version, and does not apply to current production (3.2.2) or 4.0 early adopter versions: Re: Lost my connections.
SQL Developer Team
Sql developer ver 4 , JDK ver jdk1.7.0_40
Try, Window > Reset Windows to Factory Settings