As a knowledge worker, I've found that there is no 'best' way of organising information. It depends on what it is that you're doing.

Having said that, the things I come back to are Trello (Kanban-style boards), Pinboard.in, a personal wiki, and Google calendar. I like everything web-based so that I can access things wherever I am and whatever device I choose to use.

Over and above that, I use a paper-based daily planner that I've iterated over time. I pull everything to do that day on to it, then bin it at the end of the day.

Version 3 is here: http://www.slideshare.net/dajbelshaw/dougs-daily-planner-v3 (CC licensed)