During the time I have been working with a development team, we have collected a set of online tools that help us manage our Scrum process. Some of the tools are:

http://funretro.github.io/ : Allows the team to perform better retrospectives by "anonymizing" the retrospective items. Some Engineers are shy by nature, and this tool really helped improve our retrospective process.

https://tools.wmflabs.org/hatjitsu/ : Hatjitsu is a tool for story pointing (using the fibonacci "cards"). Very good for distributed teams.

https://www.phacility.com/ (Phabricator / Phalacy) : An "all in one" development platform. Useful for pre-commit reviews, Scrum sprint board, bug tracker and others. Very useful and free.