Don’t get me started. I’ve spent a lot of time on this subject, looking for the perfect tool. Oh. Too late.
Ulysses is great, but so is another Andy favorite, Scrivener. Both are based on an older tool called Zettlr, which is inspired by (rabbit-hole warning) the Zettlekasten method.
Evernote used to be a good choice, but it’s become pretty expensive and I fear for its future. A lot of people like Bear - it’s very simple, as is SimpleNote or even the free Google Keep, which keeps getting better. Microsoft’s OneNote is powerful, but maybe overkill. At least it’s free.
I would take a look at the free and open-source Joplin. I think it has a lot to recommend it. It’s cross-platform and supports a number of cloud services for storage. It’s in active development and is feature rich but easy to get started with.
As an old-schooler, I really like emacs’s org-mode. But it takes a bit of finger training. I maintain my markdown-based blog with emacs and Tramp-mode, or with Panic’s Nova, which is a great Mac-ish all-in-one solution (markdown editor, terminal, sftp, etc.)
On the web Roam and Notion are, I think, very exciting tools with a new paradigm that works quite well.
On the hardware handwriting side, I’ve been playing with the expensive but nicely designed, Remarkable2 e-ink tablet. It has excellent integration with iOS and macOS. And when it comes to that, there are a ton of iPad choices like Goodnotes, Noteshelf, and my favorite, Notability. But you have to have an iPad. On the upside, Notability will record audio that links to your notes, which makes it excellent for note-taking during lectures.
I would recommend choosing something that provides portability - so you can move from tool to tool - is free or inexpensive, and cross-platform. Open source text-based solutions are probably the best; you don’t want to be stuck in a tar pit with all your notes. And learn markdown - so many of these tools support it and it’s a great way to created formatted, structured documents in plain text.
Note taking is very personal, and it’s worth trying a bunch of tools until you find one that fits your style. My journey is ongoing and probably everlasting!