Update: I have presented a clearer model to help search engines index your Flash content with a minimal work.
Bad referencing in search engine is the only point that really bothers me with Flash.
Why is it so hard for search engines to understand Flash content?
Because it’s not text like they use to read it, it’s vectorial text or imported text, search engine mostly see the swf (swf = flash files) like an “image” or like something they don’t understand.
Official solution: using the tags :
‹!--url's used in the movie-->
‹!--text used in the movie-->
But it seems to be a very little help in that issue.
Another reasons is that search engine follow link and as they don’t understand the link in swf they just don’t see all the structure of your swf.
So what can we do for them?
I would say that it’s important to separate the content in different swf that would be loaded in a main swf. If this main swf is loaded once in “a.html” you don’t need to load it again in “b.html” (because it’s in your browser cache), which allow us to make our swf having a structure like: “mygreatdog.html”, “mygreatcat.html”, “blabla.html”. Doing so will make your site more understandable by search engines (who care about the page name), and as a bonus it will make the back and forward button works naturally.
To make your page understandable for search engines and with Flash on the same page is quite easy finally: my way is to make a transparent swf
‹param name="wmode" value="transparent" />
that would go over the content (placed with CSS) that must be understand by the search engines (like the title, some keywords or any important text). So in this case Flash is more here only to beautify your web content (which is not the main purpose of Flash or is it ?).
Last bonus, your flash animation will be understand by the search engines, at least what you want them to understand.