The Default Popup Menu

This is the popup menu when you click somewhere outside the structure.

Implicit Hydrogens On all/Off

Here you can show hydrogens on all or no atoms. Note these are settings which can also be achieved by choosing "Explicit Carbons" and "Show implicit hydrogens" in Edit->Preferences.

Clean Structure

This lays out the structure according to standard rules (Structure Diagram Generation).

Cut

Removes the atom clicked on from the drawing and puts it into the system clipboard. Paste can be used to use it again.

Copy

Copies the atom clicked on into the system clipboard. Paste can be used to use it again. JChemPaint uses several formats (SMILES, mol, CML, SVG) so you should also be able to paste it into other programs (depending on abilities of the program).

Delete

Removes the atom clicked on from the drawing. It is like cut without using the clipboard.

Select

Selects and marks the atom clicked on, so that it can be deleted, etc.

Select All

Selects and marks all atoms and bonds in the molecule, so that it can be rotated, moved, deleted, etc.