The best replacement for jira is bugzilla.

The best alternatives to jira are rated as following:
★★★★★  bugzilla
★★★★  fogbugz
★★★★  rally
★★★★  redmine
★★★  tfs
★★★  trac
★★★  basecamp
★★  pivotal tracker
★★  confluence
★★  asana
★★  trello
★★  clearquest
★  versionone
★  github
★  quality center
★  youtrack
★  zendesk
★  jira agile
★  mantis
  rtc
  assembla
  ms project
  unfuddle
  rt
  ontime
  remedy

Your alternative for jira is not listed? Suggest!
Speaking about jira, one probably shouldn't forget about greenhopper.

Other search terms related to jira and their ratings are:
★★★★★ greenhopper
★★★ github
★★ jenkins
★★ subversion
★★ confluence
★★ stash
★ agile
bitbucket
testlink
zephyr
You have in mind a companion for jira and it is not yet here? Propose!



Google Trends

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jira
bugzilla
fogbugz