Here's a list of things that I caulk in, starting at the top;
1) Soffit joints.
2) Soffits to the fascia boards.
3) Soffits to the siding. This could also be the freeze board, typically a 1×2 or 1×4 wood trim board.
4) Where two pieces of trim meet. Example corner boards.
5) Siding butt joints and where the siding meets the trim.
6) Around all windows and doors.
7) Brick or stucco to the trim or siding. Use a paintable clear caulk.
8) Any major cracks in stucco.
This should be about every place that will need caulking. Never caulk siding to siding. Example, caulking the lip of one piece to the face of another. This will cause rot and other problems in the future.
Do not caulk in every crack or gap around the house. Your house has to breath. It all depends on the type of trim, siding or stucco and windows you have. You will have to use your best judgment.