Apart from the documentation system, I personally prefer their UI (it feels more "modern"), the fact that a support conversation looks exactly like a very classic email conversation to your customers (no issue number in the email's subject, no specific signature or structure in the content etc), and Helpscout's team have always been helpful and nice so far. The API is pretty complete as well. We're using it only for support conversations nowadays, so I can't comment on the knowledge base features etc.
We really like the documentation features as well; again, very thorough.
The one thing we really wish was there is custom field support on customer records, but Helpscout does workaround this by letting you set up a webhook it'll hit to present more information inline.
Additionally, the chat-based interface gave our customers the expectation that they'd always get an immediate response, which just wasn't always possible.
We still have it and use it for some features like usage analytics, but it's not our primary support tool.
For smaller teams, I love Front.
In looking for things that will likely work better for larger teams (10-15+) Help Scout and Groove are both pretty appealing.
Desk.com is like Zendesk in that it tries to "do everything."
I haven't evaluated it fully, but a lot of people love Intercom as well if you want to do in-app/on-site support.
Helpscout is invisible to the customer, but more than adequate for our needs. Our only pain point is it's got bad trello integrations, so we're building our own.