For me, org mode becomes a note taking and link dumping ground. I let JIRA be my todo list, and throw notes and links to different files in my org-mode file. The problems I have is when there's personal notes that should probably exist in the JIRA cards for others to use.

EDIT: I also have been using it for documentation. Github parses orgmode files, so its useful for me and the rest of me team in these cases.