Pros
Probably the most fun company that you'll be around. There is politics, but for the most part, you are valued for what you have to contribute to the table. The amount of transparency is staggering: it's not every company where any Joe Blow can query the company data warehouse or simply ask what the top secret project is. Atlassian has some of the best people working for it that you'll ever find, and I genuinely look forward to coming into work. It's exciting times, if you like building new stuff or breaking new ground, and I've not stopped learning since I've gotten here.
Cons
Like many companies that are explosively growing, things don't always scale up fast enough. Like many of the other people here, I'll point out that not all is right with Kansas, and there's some spring cleaning that needs to be done of some of the cruft. I would say that there's a lot less cruft than I've seen elsewhere, but I'll certainly acknowledge that it exists. For other cons, it takes a tremendous amount of energy to course correct, though this is kind of a first world problem. Most other companies wouldn't even offer you the option to course correct, but Atlassian does-it just takes a lot of patience and asbestos suits. Compared to the outside, Atlassian compensation kind of blows, but there are some nice perks to make up some of it. It really is a pleasant place to work, but you can make more elsewhere.