Ten years ago I made exactly this migration for a SaaS shop's helpdesk & dev team. At the time JIRA was easily the best value & most customisable solution for integrated ticket tracking. I learned Java & Groovy to write extensions for it. It wasn't just CTO/CIO friendly, JIRA really was the great choice at the time in both UX and ease of implementation. Especially if you'd been bogged down hacking RT or GNATS or permanently scarred by anything from Rational.
What I realised is that eventually they're all ad-hoc, informally-specified, bug-ridden, slow implementation of a workflow engine and metadata service. Your choice is mainly of the interface and domain-specific layering violations.
Troll-friendly soundbite: Atlassian is the new Rational.
"You either die a hero, or live long enough to see yourself become the villain"
Let us know anything specific you'd have us improve - love to know what changed over the last 10 years to make you change your mind.
> I learned Java & Groovy to write extensions for it
For the last 3 months, Groovy has been officially known as "Apache Groovy".