What is a good plan for building cube bookcases with basic tools?
Congratulations on building your own book case. Here are a few tips.

Get a good large framing square. This tool will help you scribe square guide lines and also can be used as a guide for your circular saw to cut nice straight and square pieces of wood. 

Use tiny head, counter sunk finish screws and wood glue to secure the pieces.

Make the bottom and top horizontal pieces full width. Fit the vertical upright pieces between them. Fit the shelves between the upright pieces.

Carefully measure and scribe the bottom edge location of your horizontal shelves on the vertical uprights.

Clamp a straight guide to these lines to help align the shelves to your lines before securing them to the sides.

Drill and countersink pilot holes for your screws so you won't split your wood.

Use glue on all joints.

Install a back or at least small 90 degree triangle pieces of wood or thin plywood on the back four or any parameter corners to assure your case doesn't rack or lean sideways when loaded.

Measure twice or three times, then cut once!!!

Fill your screw holes with lightweight spackle, sand smooth, prime, paint and enjoy.

Good luck