I usually just look for the .swf file in the html code and download it that way. This works, but I'd imagine there's probably an easier way.
I usually do it to play simple flash games full screen. What are you trying to do?
EDIT: Ok... this might sound stupid, but what exactly do you mean? Do you want to download the flash file or prevent the flash file from ever displaying?
You need to use a program... the only one I know of is called tubesock. It isn't free, but the demo allows you to encode up to a minute of a youtube video. I think the full version costs $10.
In Safari, open the page with the YouTube video you want. Open the Activity window (Option-Command-A) and look for the largest item that loaded...I think it has "get_video" somewhere in the URL. Double click that and it will download. Tell the OS to use VLC to open the file, and there you go!
you can download youtube vids by using either greecemonkey (there are scripts that let you download the .flv files) or by using a plugin like videodownloader. both will download the flv file. you have to convert it by using somehting like isquint or media hub