Unfortunate that they don't offer the software itself; I could use this at work, but I don't think we'd be allowed to use it on an external server.
"Etherpad Lite" is built on node.js which to me makes it more desirable from a developer standpoint for a number of reasons, mostly for the same reasons one would generally favor node.js over Rhino, so I would definitely look into that one first. https://github.com/Pita/etherpad-lite
Hackpad might have a few advantages but the basic concept of tracking individual changes with colors is built-in to Etherpad and Etherpad Lite.
Maybe there is some space in the market for a B2B company which could package up software like this for deployment within the firewalls of the ultimate customer...
On the plus side, you can charge them lots of money. On the negative side, it's not as easy (or cheap!) to market to these people and take care of their needs.
If something better came along that helped us rather than slowed us down it would be fantastic.
JIRA is absolutely terrible as well. I can't express in words how much I hate and dislike JIRA, it's horribly slow and bloated user interface and how complicated it makes certain tasks... using it as an Agile tool makes it even worse especially with Greenhopper the add-on.
Having used Bugzilla, Trac, Mantis, MediaWiki, and several other tools I 100% prefer Jira and Confluence...
(Mantis might have less capabilities than Jira, but I almost enjoyed working with it. That might have depended on the project. [Edit: On consideration, Mantis was simpler and didn't make me scream from pure hatred.])
I tend to use Trac most.
Confluence is very stable. We have a ton of content in it, and without it we are completely dead in the water. It works well.
Yeah the tags are a bit ambiguous, but I have never seen the tags get in the way. Downtime would get in the way much more.