Are you trying to import a non-Eclipse based Java project into Eclipse?
You find a lot of tips in the internet which tell you that you should create a new Java Project and then use the “Create project from existing source” option.
For example on the Google Plugin for Eclipse webpage.
Unfortunately this option does not exists. To my knowlegge the correct (and unfortunately a bit complex way) is to create a nwe Java project, select the project, right-click on it and select Import -> File System.
On the following dialog you can select the directory from which you want to import and also if existing resources should be overriden.
I hope this helps.
Remark: For Google App Engine with Java you also need to set the output path (bin folder) of the project to “projectname/war/WEB-INF/classes”.