There are several ways to make Flash search engine friendly. The main reason they don't get indexed well is that when Google spiders start reading the page (the html) it will get to the <Embed....> tag, which is where the html inserts your .swf or Flash movie, it will basically stop and fail to read the rest of the page.
The first way to help this is to actually insert meta tags into your Flash movie itself. When you open the publish settings for your movie there is a text box for your meta tags, just insert all your keywords into that and the spiders will read them before it gets into your graphics and the movie (or whatever you have in it).
Solution 2: Remember, the flash movie (.swf) actually sits upon a regular html page. Before uploading the page to your server, make sure you open up the code in that page and insert your meta tags and keywords on it. The spiders read this before they even get to your movie. *Make sure your <meta tags are inserted BEFORE your <Embed....> tags. Remember, that's where the spider stops.
Solution 3: If you are using CSS you can actually have the flash movie sitting atop a regular html page - i.e. if your visitor does not have flash installed or the movie doesn't download for one reason or another, they will see a regular html web page. There are tricks involved with doing this but as far as this thread is concerned, think about this aspect of it: As soon as google reads the </style><link href="css/...blah, blah, blah - that's where it goes. If all your tags and keywords are on your css stylesheet, it will read that first before it gets to your movie (Embed...). Remember to have your style tag before the embed.
You can always move your embed tag to the bottom of the code in your page, this is good practice as the spiders will read everything else first.
For those non-coders:
Embed is the html code tag that inserts your movie (.swf) into your page
Meta tags are the keywords for your website
and a spider is what we call the little robots that search your site for google (and all other search engines)
There are more ways but these should get you started. Hope that helps.