Desktop publishing ? Nope
IDEs ? Nope
CAD ? Nope
3D modeling ? Nope
Mathematical tools ? Nope
So which ones ?
IDEs? here's 13 of them: http://www.hongkiat.com/blog/cloud-ide-developers/
CAD? tinkercad, etc. This one is a classic Christofferson innovator's dilemna. Cloud CAD is the obvious way of doing 3D printing, which can & will move up to eat the big guys.
3D modelling? Clara.io, Lagoa
Mathematical Tools? Good question. A quick google found this, http://www.ms.uky.edu/~statweb/ which is 14 years old... I'm sure if I had a better idea of what to google for, I could find something better...
Most likely none.
How many work without an active low-latency internet connection?
Again, most likely none.
How many lock you in to their service?
Probably not all, but I'd seriously doubt "none".
Google Docs is the most obvious example of this -- I don't know anybody who uses Microsoft Word anymore. Obviously I'm in a little bit of a bubble that way, but they've certainly got a large enough user base to grow from.
Google Docs works while offline, and the same techniques could work on the competitors I mentioned.
In terms of lock-in, all of the services I listed are in the "underdog" phase of growth, where lock-in does more harm than good -- a good interop story with their competitors is more important than the benefits of lock-in. Of course, if they ever reach dominant status this might change, but at the moment, all of the ones I'm familiar with have good & prominent import & export options.
My old job used to use Google Docs, but I always felt like I was working against it rather than with it, and I know I wasn't the only one - still a lot of .docx, xlsx, odt, etc being sent around and on fileshares despite the policy being to hand over sensitive company data to google.
The main problem websites solve over native is the fact you only have to build the app once and it works everywhere (mostly). Of course, there will always be a place for native apps, regardless of desktop or mobile, when performance matters most.
I think you are already starting to see it happen actually with mobile-first web frameworks like Bootstrap, some mobile browsers performing well (i.e. Chrome), and 4G rolling out. But it is definitely just starting assuming I am right.