There are a number of resources that I have found useful in thinking about productivity processes and tools.
My productivity system is working fairly well at a few levels: I feel like my day-to-day and weekly tactical planning are in good shape, as well as my pipeline management and some medium-term planning. However, there are a couple of notable holes that I'm still looking to fill.
I spent the day yesterday at the NSF CISE CAREER workshop. It was excellent, and I strongly encourage any young US CS faculty to go to a future installment or watch the online videos if a CAREER proposal is in their future.
In previous articles, I have written about how I organize my own personal productivity. However, many of my projects are collaborative, and physical paper doesn't work very well for sharing task lists.
Earlier, I wrote about the notebook I use for planning and tracking my daily and weekly work. It's great for the low-level tactical aspects of productivity, but is not very good at long-term planning. I've tried to use it for that — semester planning pages and similar ideas — but it has not been very effective.
To manage the birds-eye view of my work, I use a Kanban-style board made of Post-It notes and painter's marking tape on the wall of my office.