Back in the late 1990s and early 2000s I experimented with a number of complex rich text, database, and proprietary formats for my notes files. It was a disaster in terms of long term accessibility. Since ~2004 or so I've used exclusively a single plain text file with embedded filepaths if media references were required.

This has worked far better and now offers a remarkable resource for both nostalgia and getting stuff done. It's huge and search is pretty much the only way through it but I still add every day.

Plain text is best. I feel that even using vim to automate time stamps is too complex. I just write it once by hand. It's easy and literally takes half a second.