If you don't mind using a command-line tool you can use ffmpeg. Using the overlay video filter:
ffmpeg -i video.mp4 -i logo.png -filter_complex "[0:v][1:v]overlay=main_w-overlay_w-10:10[filtered]" -map "[filtered]" -map 0:a -codec:a copy output.mp4
- [0:v] refers to the video stream(s) of the first input (video.mp4).
- [1:v] refers to the video stream(s) of the second input (logo.png).
- main_w is the width of the "main" input (video.mp4).
- overlay_w is the width of the "overlay" input (logo.png).
- The audio from video.mp4 is stream copied instead of re-encoded.
This example will place the logo in the upper right: 10 pixels from the right side, and 10 pixels down from the top. See the FFmpeg and x264 Encoding Guide for getting a good quality output.