Microsoft Communicator. If you're in a big company that already uses MS Exchange for emails then it's a pretty easy integration. Probably not a great solution for small companies due to the cost.
Private Jabber/XMPP server.
We predominantly use our feet. Unless someone's snowed in, sick, or subcontracted (and not local) we just walk on over to their desk and talk. Or, hold an ad-hoc meeting. When someone's physically absent from the office, we have no standard policy (though Skype is common).
http://talkerapp.com/ - to me it's essentially Campfire but free
Skype is good too but be careful if you use it for IM. I frequently receive messages hours after the other person sent them, even if we're both online. This is starting to make me not want to rely on it other than for voice/video.
Lync.
Pros:
-Outlook Integration
-Screen Sharing
-Decent UI
Cons:
-Literally the worst copy & paste implementation I've ever seen.
-No third party chat protocol integration. (I want to integrate Facebook and Google's Jabber).
Edit: Formatting.
We used skype at my last shop and it was not very smooth. I prefer self-hosted jabber / XMPP.
My company uses Communicator. Not a big fan TBH.
A stupid configuration prepends an underscore to urls, preventing it to be clickable. Hate it.
At my last company we made heavy use of Yammer.
We use Google+ for loads of internal communication. It's easy to restrict posts to our organization via Google Apps.
While I've not seen any use to adopt G+ in a public way, it's been a phenomenal internal comms tool for async sharing, discussion and debate that isn't critical enough to go on an everyone@ email list.
Pros: integration with PT and Github rules; mobile client is better than decent.
Cons: transcripts/history can be wonky; no way to add metadata to file uploads; native OS X client seems to randomly eat characters when typing.
Why is 'email' not an option? Which is by FAR the most commonly used internal communication system - although I do NOT recommend it!
Humbug: https://humbughq.com/signup/
Still pretty new, and in closed beta. But it adds an interesting threading/topic model onto the typically chaotic stream of most group chat apps.
Flowdock. Holy moly Flowdock is slow. Have to restart it a couple times every day. SO ANNOYING
Internally hosted Jabber/XMPP for chat; Google Hangouts for cross-location meetings.
Internal XMPP. Poor ejabberd isn't handling our growth in traffic very well and gets oomkilled and/or swaps itself to death with depressing regularity, so we're trying prosody (over the protests of the internal-IRC faction).
VoIP, email and very occasionally an internal messenger. The idea is not interrupting others too lightly, since we already have scheduled meetings. If something needs dealing with urgently, then these measures kick in.
Phones... and long, agenda-less, ad-hoc meetings.
And sometimes XMPP.
Dont believe there is no QQ :D http://im.qq.com/online/index.shtml
I had to choose Lotus Sametime. Now I must go weep alone.
Gtalk/Hangouts, a little Skype still, and Whatsapp (although I'm forcibly trying to replace Whatsapp with Hangouts).
We use the product we're working on: http://kona.com
IRC with about 5 users, the rest just drop in at any time and expect every detail of the discussion to be remembered.
Now using Kato.im a lot and loving it. Have used Google, Campfire, HipChat, Flowdock in the past.
Flowdock for chat and a GH/Jenkins/Jira feed. Google Hangouts for meetings.
I hope selecting two options was ok. We use a combination of IRC and Google Hangouts.
At Mashape, we use Flowdock
We love Jabber. ejabberd is surprisingly simple to setup and get going.
Flowdock, it's great.
We use Google Talk.
My setup is LimeChat -> Bitlbee -> GTalk.
Teamtinct.com - It is still in its early days, but works great.
Cisco WebEx Connect
AIM. It's so old, the NSA forgot about it.
IBM's SameTime (part of Lotus Notes).
Anybody using Sococo? https://www.sococo.com/home
We use AIM.
SneakerNet and XMPP
kato.im
http://www.templeos.org/files/TSGodSetUp.zip
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Hipchat with my close internal team. Gchat for the rest of the company.
We use a combination of Socialcast and Google Hangouts.
Internally hosted Jabber/XMPP. It's actually been one of our longer lasting decisions, so it was a probably a good choice.