SlideShowPro (http://www.Slideshowpro.net) is what I use. It’s flexible, it’s got a nice easy menu, and it’s professional looking. It handles FLV’s fantastically and allows you create a selectable menu of all playable video’s, plus thumbs and video previews. I’d go check the demo out on the homepage and select “Video Shorts: Slow Motion” and see what I mean.
I have had good success with wimpy AV. They have a new product out called wimpy rave that is skinnable. What I like about this solution is that it is simple, requires no Flash application, and the code is generated for you. Simply paste it into an html box and you are good to go.
My primary business is as a videographer, so I generate the FLV files from Final Cut Pro, set them to the size I want, and use Wimpy to display them on my site. The file is served from my ISP website so I have total control over the end result.