Right, but they don't have a good reputation to start with.
Somehow the only good things I heared about them came from people who made their money by building stuff they wanted to sell on the Atlassian platform. People less biased always choose alternatives.
I can't say much about them myself. I only used Bitbucket, because of the free private repos. Their UIs are pretty mediocre, but I use it via Git cli, so it doesn't matter much for me.
So as a counterpoint. I used BitBucket a lot before Atlassian bought them. They were great, but toward the end suffered significantly from load issues.
After Atlassian bought them:
* The service I paid £5 a month for became free
* The stability issues started to improve in a dramatic fashion
Today Stash is a great product (IMO), and BitBucket has really improved from having great Jira integration.
I was actually sad because I couldn't justify paying for the premium features (multi-person private repos) in the same way, because it was nothing I needed. It was the best £5 subscription I ever had :)
I'm in a similar boat. I kinda disliked Atlassian because of my experiences JIRA.
I generally prefer Bitbucket over Github now (was a paid subscriber of Github). I basically use Bitbucket now for private repos and Github for my public repos, since Github does seem to be the place to put open source projects.
If my Bitbucket needs ever reach the point of having to pay for a subscription, I'll do it gladly.
As far as ticket / issue tracking systems and wikis go their products are quite decent.
JIRA has its quirks but it's very flexible and customisable. Its UX is also quite ok for such a complex piece of software. Keep in mind they're competing with stuff like SharePoint and downright UX atrocities such as HP ALM.
Confluence is among the best enterprise wikis targeting end users (i.e. users not familiar with Markdown), too.
HP ALM is awful. The biggest issue is that you needed to install it on the client machine to be used as a plugin. I would rather have Atlassian products than HP ALM and Clearcase!