Blender is a free and open source 3D application that has many features including a video editor. This guide is based on Blender v2.78.

First, change the default 3D to video editor, and the graph to properties editor.
This is the main layout we'll be using. If you want to restore the default, use File > Load Factory Settings.

Properties values should be set before inserting a video, especially the frame rate that should be the same as your source videos. Recommended settings for YouTube : support.google.com/youtube/answer/1722171 . This is an example for 1080p @ 60fps :
The audio sample rate is 48000 Hz by default, you can set it up to 192000 Hz on the Scene tab. Keep your preset by using File > Save Startup File.
We are using a MKV container instead of MP4 because of the FLAC audio capability.

Click Add > Movie / Sound / Image etc on the VSE menu. Make sure the framerate on Properties is exactly the same as your video framerate. Green is the audio, blue is the video.

This is a few list of hotkeys that will be used frequently. One of the editor area needs to be active by hovering your mouse cursor above them.

L / M / RMB : left / middle / right mouse button
MW : mouse wheel


Soft cut : frames outside cuts can be recovered through changing the strip duration.
Hard cut : no frames outside cuts can be recovered.

To be able to view frames accurately, you need to click the "Refresh Sequencer" button (on the vse panel) at each cut-points.
Or convert the video first into raw / mjpeg / all i-frames (gop=1) then do the cut. Example / a quick way via ffmpeg :

Using color effect strip :
If strips blending mode doesn't work as expected, try to change it to "alpha over".
Fade in / out can be used for audio too by setting up the volume with keyframes.

After you're done editing, make sure the start & end frame are set. Render the video through the Properties panel.


If you want a better result, render the video to lossless with audio separated as wav from Blender, then do the final convert on your preferred editor (Avidemux / Handbrake / etc). The quality difference is very noticeable on low bitrate video. You just need a lot of space for the lossless file.
If the lossless file can't be opened with your editor / wrong color / etc, use ffmpeg to convert (see commands above)

Blender Manual
https://www.blender.org/manual/editors/sequencer/

Mikeycal Meyers's Blender Video Editing 2.7
https://www.youtube.com/playlist?list=PLjyuVPBuorqIhlqZtoIvnAVQ3x18sNev4