For instance, we're an Atlassian shop through and through; we also use Fisheye, Crucible and Bamboo. As such, we wanted to tie all of these apps up to Atlassian's SSO solution (Crowd). Take a look at the integration guide for JIRA¹. The process can require finding missing JARs, editing Java property files, commenting and uncommenting forests of XML, and then you're still subject to a bunch of arbitrary restrictions around group membership (super fun when paired with AD). The whole thing feels like an afterthought that was never given the respect of a proper feature.
I personally get the impression that Atlassian's product codebases are pretty fragmented as a result of their grow-via-acquisitions strategy. On the front end, the products are good looking and usable. On the back end, things are a mess. Still, it's my job to run the mess, so I'll keep slogging.
¹ http://confluence.atlassian.com/display/CROWD/Integrating+Cr...