I don't know a way to do this en mass, but if you delete all imports from a source file and then right click in the source editor, you can select fix imports. This will import all the classes for you alphabetically, asking when it encounters package ambiguities.
As Soldier.moth pointed out, Netbeans will point out other issues, like casts and override annotations, in line, by use of a light bulb to the left of the source.
The equivalent of Eclipse's "Code Cleanup" in NetBeans is "Format". It's under Source > Format, and the keyboard shortcut is Alt+Shift+F (on Windows). Unfortunately, unlike Eclipse, it doesn't seem like this can be configured in NetBeans.
Fixing imports For a single file, namespace, or project (depending on what's selected in Project window or has the focus): Source > Organize Imports (to sort and remove unused imports) or Source > Fix Imports (to sort, remove unused imports, and add missing imports). Or during every save: Tools > Options > Editor > On Save > Organize Imports.
Removal of trailing spaces For a single file (place the carret in the code file): Source > Remove Trailing Spaces. Or during every save: Tools > Options > Editor > On Save > Remove Trailing Whitespace.
Code Format For a single file, namespace, or project: Source > Format. (Customize the rules in Tools > Editor > Formatting). There is also a plugin called Jindent you can install (I have not used it myself). Or during every save: Tools > Options > Editor > On Save > Reformat.
By default, Netbeans will display hint icons next to problematic lines of code and in the scrollbar, allowing you to perform an automatic fix if desired. These can be configured via Tools > Options > Editor > Hints. Netbeans can search all problems in the project using Source > Inspect. Or, to reiterate, many of these problems can be batch fixed with Refactor > Inspect and Transform.
If you just want to make your code have proper indentations on a whole project, simply click the project name, go to "Source," and then click "Format." Hope this helps!
Right click on the project (or a package if you want), then choose "Inspect and Transform". In the dialog box, choose "Organize Imports" , from browse choose imports --> then --> Unused Imports