I have used Jira and nTask for several teams. I like both, and they each have pros and cons. I am a huge believer in developing a team's process outside of the tool they plan to use and then customizing the tool to fit the needs of the team. I have worked with teams that went the other way around, and they experienced a lot of inefficiencies and pain points because they believed they needed to manage their work to match the tool they used.
Excel, notecards, and sticky notes have all proved themselves to be valuable facilitation tools as well. I think the main thing to consider is the size of the team, the logistical requirements, and the accessibility of the information. Notecards work well for brainstorming with teams who work in a shared space, but that approach fails when a team is virtual or does not have a shared space to work in regularly.