You can use any stage size. You just have to use the publish settings under HTML tab as follows:
Scale: No Scale
You can use stage.stageWidth and stage.stageHeight to get the width and height in pixels of the stage when its in the browser.
Edit: Sorry stage.stageHeight/stageWidth is for AS3. Use Stage.width and Stage.height instead.
in the browser I use swfobject v2 and just set parameters to 100% for height and 100% for weight