I ended up using spreadsheets for keeping track of todos and habits. LibreOffice Calc is the obvious solution for FOSS, though I am using Googles Spreadsheet for cloud syncing and the Android/iPhone apps. If I get trouble with Google I will just copy and paste to LibreOffice and I am good.
For notes, IMHO nothing beats a good directory structure/layout and markdown. (Sorry, org-mode guys. :-P )