Setup in 2021
Currently I am comparatively happy with my app setups, which I basically have finetuned during most of my PhD degree. It will probably change at some point, but well.
For task management, I am using OmniFocus. While pretty heavy and certainly a time sink in terms of setup, I think it has some indispensible features. The flexibility comes with its downsides, but I certailny appreciate that I can tune it to my needs. Next, the way OmniFocus treats defer-dates, paused-tasks, and reviewing is crucial for me. Everything which is more far away than 1-2 weeks is either deferred or paused, meaning that I will never be distracted by 90% of my database.
Lastly, for privacy reasons, I appreciate that it uses End-To-End Encryption for my database, which almost no other task management app provides.
For knowledge management, I am using Obsidian and DevonThink.
I started doing something like a Zettelkasten, but for me this did not really work out. Rather, I now built something like a personal wiki in Obsidian where I sort out my thoughts. I built some hierarchical structure and all new thoughts are then put somewhere into the tree.
For all non-text files, I put them into DevonThink. Basically, I archive them for long-term use. Devonthink makes it easy to create unique links, which are available cross plattform (also on iOS with DevonThink To Go!). Then, if needed, I can link to them in Obsidian. I have a setup where the Markdown files are indexed in both apps, having them available for backlinks etc.
Roughly, Obsidian is “my own thoughts” while DevonThink is “archiving” –the latter is used both for my own materials as well as those of others (literature, etc.)
Going back to privacy, both Obsidian and DevonThink support End-To-End Encryption of your databases.