I've donwloaded some youtube videos that I want to join. I joined them with mkvmerge, but in the joined video, there are ~5 seconds skips (in VLC the second counter stops and then jumps 5 seconds) at the start of each video I joined (even at the start). Is there another way to join them so I won't have this problem?
Try a video editor like Lightworks to join them into one video, there you can cut any black frames and won't have to deal with possible glitches introduced by muxing different videos into one stream.
If your videos are indeed webm and not h264 you might need transcode them into another codec (f.e. with ffmpeg), a production codec like MJPEG or any lossless codec might be suitable as an intermediate codec so you don't loose much visual quality after exporting your finished video.