HipChat - Small user base and unscalable architecture. Hundreds of thousands of users and loads of resources to rewrite nearly all of it's backend. Still a work in progress but it's been very stable for the past year and the clients, which were all non-native web views, are coming along nicely.
Fisheye/Crucible - Small user base, unprofitable. Now has thousands of users and is hands down the best code search and review tool that lots of people don't know about.
SourceTree - Massive expose for a very small tool that wasn't well known before acquisition. Many new features, has remained stable throughout.
Greenhopper - Was a small, profitable, plugin. Now built-in, completely integrated hundreds of new features and has adapted well to various trends in Agile (scrum, kanban).
Despite this thread, which shows HN's consistent (and ironic) distain for (or is it lack of understanding of?) successful software companies, Atlassian is actually great at creating great products out of questionable acquisitions.
Outside of Atlassian:
Whatsapp is free now, people like free. That's neat. To people crying out privacy, honestly… privacy is the only thing that VC backed b2c companies sell that's actually worth real money. They were eventually going to open that pandora's box.
Twitch gets to continue existing and it's ad-free for prime members now as well. I like free :).
Firebase is better than ever. Let's all cry a single tear for Parse, we all wanted a massive Mongo cluster backing our data, right?