* BitBucket (core app, private)
* GitHub (FOSS projects, public)
* Trello - tracking progress
* HipChat - IM
* Basecamp - dates, discussions, project type stuff
* Google - docs, shared calendars, Hangouts
* Screenhero - screen sharing
We've almost managed to remove email from our daily flow - I very rarely send / receive internal emails now.
HipChat + Trello have become our foundation tools - couldn't live without them. (The new Trello attachments view has plugged a gap, and made sharing designs much easier than it used to be.)
HipChat is brilliant once you move on to building stuff - plug in code commits, deployments, customer service (we have Zendesk alerts) etc.
I would absolutely agree with your last point - sharing links + discussions around links is the biggest problem by far - Google+ is a perfect fit, but (our) people just seem resistant to it. I've tried, and failed, several times to get everyone to adopt it. We have a bunch of iOS people and they often share direct from Flipboard, which may be part of it.