The parts tree and connections tree are loaded from two XML files.
Inside your TinkerCell folder, take a look at PartsTree/PartsTree.xml and PartsTree/ConnectionsTree.xml
The PartItems folder contains the files to draw each part. The PartsTree/Icons folder contains the icons for each part.
To add a new item to the tree, just edit the xml file. If you do not provide an icon and/or a PartGraphicsItem with the same name, then the item will automatically get the same icon and graphics as its parent.