We used JIRA for a long time until we replaced it with something internal when we bought out another company. We switched to internal Git as well, but Stash was pretty cool, though GitHub's private repo plans aren't that bad and I always liked GitHub's functionality much better.
Plus we used some other Atlassian stuff as well, really though they make agile easy as pretty much possible, but like I said, we've replaced them internally, and eventually we'll offer these things to the public as well.
Kanban is great not just for planning, but even just for an overall view of a project if you've got your specific tasks and details elsewhere, especially useful for huge projects like an ERP.
As far as IDEs go, we use PhpStorm (cross platform), WebStorm (for our JS people), and Visual Studio (for our one person unfortunate enough to manage legacy stuff we inherited).