FFMpeg is great for that sort of thing (and used by just about everyone doing automatic conversions, apparently including youtube.
Update: Are you sure you want 'FLA" as the output? Unless you are targeting really old versions of flash, you'll likely be better off encoding to H.264.
I also wanted to add that for an individual video it's a bit of work to use and get good results, but if you're going to use it over and over it's easy because it's so easy to automate. Even when you are doing your testing it's easy to make a small script/program to encode your test videos with various options and see the results.
FFMpeg is great for that sort of thing (and used by just about everyone doing automatic conversions, apparently including youtube.
Update: Are you sure you want 'FLA" as the output? Unless you are targeting really old versions of flash, you'll likely be better off encoding to H.264.
I also wanted to add that for an individual video it's a bit of work to use and get good results, but if you're going to use it over and over it's easy because it's so easy to automate. Even when you are doing your testing it's easy to make a small script/program to encode your test videos with various options and see the results.