GreenHopper
Plugin URL: https://plugins.atlassian.com/plugins/com.pyxis.greenhopper.jira
Status: 
Compatible
Limitations: Version 1.4 of JFS has an ability to restrict user access to Greenhopper as a whole. JFS does not allow to keep an access to GreenHopper while securing time-tracking data for certain user.
Tempo
Tempo plugin has its own security system. JFS should be used along with Tempo to secure JIRA native access to time tracking data, estimations and work logs.
Plugin URL: https://plugins.atlassian.com/plugins/is.origo.jira.tempo-plugin
Status: Compatible
VertygoSLA
Plugin URL: https://plugins.atlassian.com/plugins/com.valiantys.jira.plugins.vertygo.sla
Status: Compatible
Notes: Add Java property to your Tomcat service: -Dcom.quisapps.jfs.cf_guess=true
Limitations: custom fields which are updated by VertygoSLA must have unique names across the whole JIRA instance. This means that you can not have two fields with the same name.
Jira Timesheet Report and Portlet Plugin
Plugin URL: https://plugins.atlassian.com/plugins/com.fdu.jira.plugin.timesheet
Status: Compatible