Programmatically embedding picture in video

I'm trying to figure out the best method to programmatically embed a logo onto videos uploaded from users before they are sent to a youtube channel. I'd like to do this with minimal artifacts added. The files will be uploaded to a server where I'll have both command-line and PHP access to it. It will be on a shared host, and I expect that the traffic won't be high to start.

My current thought is to use ffmpeg, however I wasn't sure how versatile that would be (with the tons of formats out there). I figured encode it at a high bitrate to minimize artifacts added and then upload to you tube.

Has anyone else programmatically had to get a logo onto youtube videos? What worked 开发者_运维问答well for you?

ffmpeg apparently has a plugin for this. However when I was looking into transcoding in general I decided it would be more fun to avoid all the arcane video permutations, and avoid the extra aggravation of dealing with long running processes. So I decided to pipe my videos through a service. Encoding.com's API appears to support logos.