I am looking for some tool that would help me prototype basic website structure and logistics (or simply user interface).
It should be extremely efficient in the matter of time needed to do simple changes like changing position of objects on the page. It should provide features for creating multiple pages and linking them together.
I don't need visual aspect of the thing, just the basic structure, placement of objects and logistics.
I prefer offline, free or open source solution.
Try Mockingbird, it's mainly used for user interface prototypes, but you can easily use it for flowcharts / structure diagrams etc.
Best of all it's free!