FMS chat vs PHP

It completely depends on your needs.

could you list out advantages vs disadvantages ?

Do you mean LiveCycle?  PHP will poll, Livecycle will push data.

What do you intend to use this for?  Without knowing that, the question is kind of like "What are the advantages of a wrench instead of a hammer?"

One advantage of doing this in PHP would be the easy access to lots of PHP developers.  However if you hang out with a lot of Flash experts, you might find Flash was a better answer.  It will all depend on your needs.

lets say i have a collaborative whiteboard...

how do normal http based calls to php from flash using using LoadVars/XML class fare against flash remoting calls to AMFPHP vs Flash media server which works on a different protocol (RTMP) .. in terms of maintianing the real time aspect of the application..basically the speed of the app...how would the 3 approaches rank ?

Here are some links to the existing science:
http://en.wikipedia.org/wiki/List_of_collaborative_software
http://www.google.com/search?hl=en&q=collaborative+whiteboard+software

Now that I understand your question, I realize I am not competent to answer fully.  I think the AJAX-type protocols that have "listeners" usually wind up with two performance issues - the speed of the internet connection and the speed of query processing on the backend.  In other words, the protocol speed is not an issue when compared to these other two factors.  So my best answer would be that you might want to choose the approach that seems easiest to program.

HTH, and sorry I cannot be more specific, ~Ray