Let's face it
When it comes to Agile Scrum, the most flexible tool one can have is a whiteboard, magnetic pins, colored markers and post-it notes of various sizes.
A whiteboard is always there, progress can be seen at a glance and burndown charts can easily be built by counting stories and issues.
But then again digital tools are more permanent, access can be given to stakeholders that are at a distance, can serve as knowledge repositories.
JIRA doesn't cut it
For classical project management, JIRA may well be a standard. Atlassian has carefully built an arsenal of productivity tools that interact well, although it is reasonable to say their price may be too high for they offer.
As far as Agile Scrum is concerned, the Greenhopper plugin feels like a makeshift solution. It's not built to really follow Agile principles, let alone the Scrum framework. Despite the terminology thrown into the labels, one needs to put some really heavy work into the workflow and maybe script a little before something marginally useful emerges.
There are many tools out there dedicated to following Agile Scrum and here are a few that are noteworthy:
Agilefant: as far as functionality goes, it's pretty great but I personally found the interface dated and clunky. JIRA's UI remains the worst in terms of bloatware but Agilefant manages to partially hide its usefulness. It's built on Java and it's a headache to have it self-hosted.
IceScrum: I love the workflow in IceScrum, especially because it enforces the Scrum way. Stories need to be in the backlog and then estimated before they are placed in a sprint. Your team members have roles and each role offers access to specific operations. There's little in term of knowledgebase but this part can be compensated by the use of a well-organized wiki. The downside? Built entirely on Java, you need a powerful server to run it yourself. You can have it hosted, but it's still slow.
Axosoft: This is the de-facto industry standard in my opinion. And for good reason: clean interface, well-defined process, Agile focus, speedy. Downside? It's expensive (but in the long run cheaper than JIRA and way much better). For the cost you get project management, knowledgebase, bug tracker, all seamlessly integrated.
There are many others out there but these are the ones I have used mostly.
Which one I like the most? Difficult question. I would use Axosoft if it weren't so expensive. I simply love IceScrum's implementation of the Scrum process but I don't have the VPS resources to reliable host it on my own.
I'm currently using Flying Donut and I quite like it. I do miss stuff from the others, but as a tool it's the closest one to pure whiteboard flexibility.