After years of frustration with task apps, I tried to migrate my system to pen and paper and... back to a task app in 2 days! The biggest pluses of an app (as opposed to paper) are quick text search and copy & paste, especially for URLs. After this experience I realized how much I depend on URLs for my daily activities: For example, to reference GMail emails, follow-ups, search results, things to read, etc... Maybe pen & paper is perfectly fine for most professions, but for techies unfortunately we are stuck with (bad) task apps for now.

Side-note: I have used so many task apps that I am embarrassed to list them here, and right now I am settled with Toodledo for the main task db and Tomboy for daily tasks and general notes. I am not totally happy with it, but at least it does not get on my way. My "system" is a combination of GTD and Covey's 7-habits that I use for almost a decade.