Recs.
Updated
JIRA is the tracker for teams planning and building great products. Thousands of teams choose JIRA to capture and organize issues, assign work, and follow team activity.
SpecsUpdate
Pros
Pro Integrations and plugins
It integrates well with a lot of other tools, including other products from the Atlassian suite. Plus there are a ton of plugins, including charting tools, screen capture, etc.
Pro Very powerful
It has many options for configuring the status roads, very good filtering, excellent way of tracking time.
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 Overly complex
Finding out how to get the simplest things done takes a long time. There are options over options that you are not interested in, that you have to evaluate just to make sure that's not what you're looking for, until, eventually, you find your item buried where you wouldn't have thought to look. Example: A simple summary of time spent on all tasks in a project.