I wouldn't be installing apps from an unknown author, but if it was on github and I could review and compile it myself I'd be a bit more inclined to try it.
Hangouts - for voice/video (standups)
Hipchat - for chat
Trello - Tasks
Google Docs - Knowledge, collaborative editing
Github - code versioning
Has anyone tried sqwiggle.com, we tried it, but we get the same thing from impromptu google hangouts for free. A truely native sqwiggle app that integrates more into what we are doing makes sense.
Thanks for trying out Sqwiggle! Solid feedback, we're working hard to make the experience more seamless with the OS. Would love to hear if you have any other thoughts or ideas. Let us know at howdy at sqwiggle dot com.
If you are talking about storing things like files etc then you could have a look at Amazon S3. If you are referring to user records etc, then use a good MVC framework (with ORM as makerops suggested).
You should check if the software is listed on the bugcrowd bug bounty list. Its a list of websites and software which accept responsible disclosure of security issues.