Made my first game, Crisp Bacon, from scratch and decided that it's a bit too much for me to handle. So, in February (I think) moved to GameMaker (multi platform & faster development) and it has given me 4 little games last month, as well as couple before that. Still miles to go until licenses pay off, tho. I'd like to try Unity one day, but it looks a bit more difficult and I'd like to get something decent/successful out from GM before comfortably moving on. Also, HTML5 export is a nice thing to have. Unity player requirement - not so nice.
Something I can really recommend is flowdock. It's amazing especially for over-seas communication. They also integrate to a ton of other tools.
From todo lists I prefer Pivotal Tracker for bigger projects.