Recs.
Updated
SpecsUpdate
Pros
Pro Combine multiple Projects, Streams and Tasks into 1 Board
JQL can be used to create filters that show anything in Jira, this data can then be used to drive Scrum Boards which combine projects/streams into 1 place. A common issue I've found in organisation are teams working in Silo's even though they have a lot of cross over. Jira can help mitigate this.
Pro Backed by a trustable company
Jira is developed and maintained by Atlassian, which is not an unknown venture, especially for developers. Atlassian has a great number of other products used by million of users worldwide, including BitBucket, HipChat, Confluence and Stash.
Each of these products have hundreds of thousands of users who use them daily and this has allowed Atlassian to garner a lot of goodwill from the dev community.
Cons
Con Changes at will
Jira changes features every few days, making the complicated UI even more confusing to work with.
Recommendations
Comments
Flagged Pros + Cons
Con Locks you inside its own ecosystem
If you use Jira you are pretty much locked inside their ecosystem. For example, if you want to add a tool to your project management stack (like a wiki) more often than not you will have to buy one of Atlassian's tools.