From your question, I assume by agile tools, that you are asking for agile tools for project management. Companies choose these tools based on their licensing budgets, existing platforms and technologies that suit their environment. For example, if the company is working with Microsoft products, then they may get some trial licenses for Microsoft foundation server and eventually start using it. Here are some of the tools that are popular in agile project management.
Atlassian Jira/Jira Agile- This is one of the more popular tool names that I know of. This tool is used for product development tracking, organizing issues, assign work and team activities. Jira handles majority of tasks as issue types. User stories, bugs, epics, new features are among the few issue types that can be tracked, managed and shared in an agile project.
Axosoft OnTime Scrum- This is a HTML-5 based tool that provides management dashboards, burndown charts along with time tracking for coding and testing.
Microsoft visual team foundation server- This works in collaboration with the visual studio as an application life cycle management server. The tool aids in management of tasks among team members that can be used in an agile environment. Developers using visual studio for development in C#, Java or other platforms would definitely prefer using this to distribute their tasks.
Telerik TeamPulse- This is another popular tool that helps manage requirements, bugs and can work with Microsoft TFS that supports Kanban and scrum. The product offers a feedback portal, product owners can prioritize their backlog while project managers plan their sprints. This can be used in tandem with TFS, where developers use TeamPulse for tasks and integrate with visual studio with TFS.
Rally- I have had personal experience using this tool for an agile project. We used a Kanban style board for managing the tasks along with the required user stories for each sprint. Rally has excellent ease of use, one can create their user story, bug, epic or task and assign the size and severity and ownership. Based on the style used the priority of the user story, task or bug is decided and pulled in or out of the current sprint.