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For 1080p video I use x265 with CRF 24 for live action and CRF 16 for animated content. For 4k you'll probably want to increase those numbers a bit (i.e., reduce quality) so the files aren't huge.

As for audio, I usually leave the audio tracks intact since I don't think it's worth reencoding them -- unless it's PCM which I reencode into FLAC to save space (or E-AC3 640kbps if I need to save even more space)

As for software, I usually use handbrake because it's convenient but you do need to set everything up correctly because some of its defaults are pretty bad (like defaulting to 30fps when there's a "same fps as source" option right there) or you can just use ffmpeg directly