Gareth is correct it can confuse more than help.

I place Flash files in a separate folder then disallow the folder in robots.txt

Then create alternate content and use swfObject to embed the Flash and alternate content.

The alternate content should be a non-flash version of the flash, say a static image of the Flash or html text of the text contained in the Flash file. All SEO/visitor/ friendly and compliant.

If it's a full flash page create a simple text only version, keeping the text etc the same as the content of the Flash file - this doesn't take long - you already have the text.... use swfObject to place your content and your done. You now have a version of your website for non Flash browsers, screenreaders and mobiles. It also prevents that "click to activate" in IE 6 browsers that aren't updated.

swfAddress allows bookmarking in the normal one bookmark=one page way which as Gareth also says is vital.

Both swfObject and swfAddress are open source, loads of info on Google.