Paul Tondeur threw togetother a little sample that shows how you can integrate Unity3D, Flash and javascript in the page fairly simply with lots of great demos.  It really is just about passing parameters around into the objects from javascript, then within Flash calling ExternalInterface to call external javascript or within Unity3D calling Application.ExternalCall.

//Flash adding callback for javascript code
ExternalInterface.addCallback("functionNameInBrowser", functionNameInFlash );

//Unity3D calling javascript code
Application.ExternalCall("javascriptFunction", "Parameter1");

Nothing too tasking but if you want to see samples of this working together from flash, flex, javascript, unity3d then check it out. Zip on over to Paul’s site to grab the files and more demos and samples. All examples are bundled in one download, which includes all the Unity3D, Flash, Flex, Actionscript and Javascript files.

Here’s some demos

• Build a Unity3D “browserchat”
• Make Unity3D objects clickable and load content in Flash
• Drag a rectangle in Flash and drag an cube in Unity3D
• Add, delete and drag objects from the Flash interface and show this in Unity3D

This teamwork to make a common kit will help to consolidate all issues with this and hopefully provide a really solid platform for embedding flash that takes into account all browser and satisfies standards but also works all the time. Making it harder to vote against when it comes time to decide what technology to use.

Of course there have been libraries like SWFAddress (for deep linking in flash and back button support easily) that have been built on top of SWFObject that will have to be switched over that have large user bases and following.

Check out SWFfix (of course this project has been very quiet and is not public since Feb 6-7th) hrm.