Just having long conversations in chat tends to not be productive, but you need chat. Something like Slack is a good choice if you can't get everyone on IRC.
Somewhat still wanting for better "whiteboard simulator" type options.
Ultimately not having an office not only saves the commute, but it saves a lot of thought-cancelling interruptions. People say this is "collaboration", but usually it's just someone being noisy in another department talking about a football game, or someone repeating the required meme / pop-culture reference to hearing a word.
The advantage of having a great home office and being able to play your own music (or not to HAVE to play your own music into headphones) is pretty much priceless.
It does require hiring the right kind of folks and being able to communicate very clearly what you want.
It's especially valuable as I really believe being able to work on what you work on shouldn't be constrained based on where you live, because that's unfair to a lot of smart folks with reasons to not want to live in the half-dozen or so major tech centers. (Or someone gets bored working for the only major software company in town).