We have about 30 people on Slack, and the DM functionality is probably the thing I use the most. It has replaced both IM and email for me. When you merge those two things, you get a one big thread that is easily searchable by keyword. Add in automatic rich media like link description, inline tweets and YouTube videos and you have something that neither IM or email has.

I've been using a tiny app called Time Tracker for OS X for the last five years. It hardly ever gets updated and doesn't look sexy, but it gets the job done (and it does work on Yosemite).