I have the same issue
http://www.onlinetvad.com/S&ETour/
I was wondering whether to switch from .flv to H264 / mov formats - i want the widest compatibility.
Flash seemed universally supported, but unless from YouTube flash does not stream to iphones / ipads / etc.
So I made a vid, exported from QTPro posted it in Apple format and it plays fine on pure Apple kit (Mac pro and Safari - or iphone ipad) but NOT on a mac running other browsers i.e. Chrome or Firefox - nor very well on any PC
I am pretty sick of this format war over online video - it is prejudicing the success of my fledgling business and has wasted a lot of my time.