There are 2 or 3 most populair flowchart designers

1st is Visio : but its not free
2nd option u can use is MS-word (add-in the draw toolbar )
3rd Ms-powerpoint allso not free

This 1 I just found (its free):
http://www.smartdraw.com/specials/fl....htm?id=140602

other u can use paint or some other tool just to make a diagram.

If you have troubble by distinguish the "content flow chart" and "site navigational diagrams", why not just type it in, in google and you'll find lots of stuff regarding the subjects.

Good Luck