That's why we initially preferred Flowdock over Slack (but I think now we have a clear winner, and I use mostly Slack)
Yep, I have. It's pretty different from Zulip.
Zulip's threading model is much more like a lightweight version of email threading -- when you start a new thread, you pick a short topic for it, and then after that people just reply to the thread.
Not exactly the same, but you may find a product I worked on a few years back, www.kona.com, to be of academic interest as someone who is looking at different communication methods.
We used a similar "topic" method and allowed users to fork conversations to have the best of both worlds -- linear chat for most cases and topical chat when a breakout was needed.
The biggest downside I've found is some people always forget to use the threading feature and comments fall out of the thread.
[EDIT]: I just had a look at Slack's implementation and I think it has some pretty cool ideas. I think being able to follow an individual thread at a high level is useful. Being able to have a conversation without bothering the whole channel is useful. I think the idea that threads are private by default is not; I think a good alternative would be to disable notifications for messages in threads you don't care about, but have them remain public.