Back in 2009, I was put on a project with a very short time frame and a lot of work to deliver. A couple of the senior developers looked at the resources and technologies at our disposal, and they realised they were inadequate for the task at hand. So we set up a completely open source solution - developed on Eclipse instead of RAD, tested on Tomcat instead of WebSphere, used SVN instead of ClearCase, and hooked into Hudson.
All this was running on a spare machine sitting on my desk. And of course, we had to keep it a secret. It all came to a head two project managers later, but it is a vindication that when I returned to the department years later, many of those tools had become the norm.
There is a term for this: Shadow IT. And it comes about because no enterprise-wide solution is going to cover everything that needs to be done. In 2009, the computers we had weren't powerful enough to effectively develop on RAD or WebSphere. ClearCase didn't give us continuous integration, and is a generally burdensome source repository compared with SVN.
(In late 2010, I switched projects in the department to one that used the official set of tools. The team had just lost 7 days to a ClearCase outage, despite it having paid support. We never lost any time running SVN.)
What surprised me about our switch to the Atlassian suite of tools is we are still in a semi-secretive state about it. It's a tool for our section, that we are meant to deny knowledge of to outsiders. The tools and their relative effectiveness are of interest to others, and better practices only come by demonstrated utility. Otherwise we're beholden to sales pitches to people who aren't directly affected by the the products being bought.
The whole point of going agile is that teams individually can reflect on what works (and what doesn't!), so they can respond for the future. Having severe constraints on their tools limits their capacity for change, thus making the exercise less effective.
For us, we are certainly benefiting from using our own tools. JIRA is far better for collaboration than the physical boards we had. Confluence is more intuitive and powerful than Sharepoint. Bitbucket has many advantages over SVN. But most of all, we've got a development team excited and engaged with the tools - a far better situation than the usual stream of complaints that have been ubiquitous in every workplace I've been in.