Im looking for a tool to help design the structure of a website to be built. I want to be able to clearly communicate what will be contained in the site when it is finished with the use of diagrams.

I am not too sure what you mean, if you mean the actual design implementation you could use something like dreamweaver. If you mean actually designing your website, prototypes are generally done one paper since they are easiest and you can test it easily with users. However I believe there is prototyping software available, google will be your friend here.

Client can always say that he wants something simmilar to abc.com ,etc , you need to learn CSS,flash ,etc.

I work with Flash, Dreamweaver, CSS, HTML, PHP, MySQL and more. :o)
Yes, paper is definitely my choice when designing the overall site (or software) structure).

What I need is something to help me draw the diagrams to communicate easily with the client. As 99% of clients are online, paper won't do. :)

What I'm looking for would be something similar to MS Visio, but not that heavy. ;)

I suggest trying google as the fastest option, if I get some time later on I will take a look for you though.

What if you make a video of your presentation? or install a webcam and point it at a whiteboard as you discuss everything to your client...
=P i dunno if that would help...

Yep, I always do a video.
Then again, I need the charts. :)

Can you use word, inserting images as needed?