Hey Katie- We don't officially support FLVs for upload (though unofficially they sometimes work). We'll be adding support for them soon. In terms of converting, if you're on a Mac I'm a big fan of VisualHub or iSquint.
I have a complaint about email alerts: The subject line on the email alert is something like "TheNinja replied to a discussion on Ask A Ninja Fans," with no reference to which discussion it was. That means if fifteen different people reply to a thread, GMail groups them by the person posting the reply rather than where the reply was posted. I'd like to see the email subject changed to something like "A new reply has been posted to Welcome Beta Testers" for more intuitive grouping. Even for people who aren't using GMail, it will make it more clear upon seeing the subject line what the reply is for.