Trello

For projects that have surpassed the "proto project/product" phase (so projects I have actually started working on, I use Trello). What I love about this is that I can take a break anytime for months, and my progress is perfectly captured. I don't need to spend time digging through the code, or finding some evernote note... it's not full agile, but just the concept of the board with several buckets and cards for each task is really helpful imo.

Here is an example from my Noobly Project: