I think you'll need to be more specific. Do you mean the
browser (Internet Explorer, FireFox, Safari, etc) will be
transparent so you can see your desktop through it? If so, then no,
If you mean can you make the swf partially transparent so
that you can see HTML behind it, then yes.
You'll have to set your movieClips or whatever else is on
your stage to alpha = 50% (or whatever transparency you wish).
Then go to File>Publish settings and under the HTML tab
you'll see a choice for window mode (this is wmode in your HTML
code). Choose windowless transparent and that shoudl do the trick.
If this isn't what you're looking for, please be more
specific in what you're trying to do.