You could check out my Pinterest boards on the subject:

Digital editorial design in general

Article layouts in particular

Storytelling pages in general

MIT Technology Review! https://www.technologyreview.com/

For more academic stories, I find inspiration in the works of:

Bret Victor

Edward Tufte

Harvard Law Review

The visuals in these are pretty spartan, but lots of good IA ideas.

I think The Intercept is doing some interesting stuff...especially in their Features.

Vox Media (and specifically The Verge) does some cool features. Both OpEd like: Welcome to Uberville and reviews like: iPhone 7 Review

Paul Ford's What Is Code? from Bloomberg is worth noting as well.

I work in Editorial design for digital. I'd love to see this thread get some legs!

There are lots of good individual articles here: https://longform.org/ some are templates, some are "art directed" but they stay current.

I want to second Designing the editorial experience" above (It's a great book!), but would add "Designing News" https://www.amazon.com/Designing-News-Changing-Editorial-Information/dp/389955468X/ref=sr_1_1?ie=UTF8&qid=1476563355&sr=8-1&keywords=Designing+news. Has some fantastic case studies in it, including one on Snowfall. https://www.amazon.com/Editorial-Design-Digital-Cath-Caldwell/dp/1780671644/ref=sr_1_3?ie=UTF8&qid=1476563355&sr=8-3&keywords=Designing+news Is also a pretty awesome.

I'm surprised no one has mentioned Frank Chimero yet.

Check out "What Screens Want" and "The Web's Grain" especially, not just for how they're designed, but for them being great articles about Design, too.

The first article that really stood out for me as being great digital editorial is/was Snowfall by The New York Times: http://www.nytimes.com/projects/2012/snow-fall/

Maybe a bit too easy as I'm working for the studio atm, but Studio AIRPORT did some fine digital editorial work last year with Beyond Prison.

http://framescollection.com/tunnelrats.html

Two resources that have helped me out are browsing Matt Willey's portfolio http://www.mattwilley.co.uk/ and also the book Designing the Editorial Experience by Sue Apfelbaum and Juliette Cezzar. There are a lot of great Q&A interviews from the folks at NYT, Huff Post, BuzzFeed and more. https://amzn.com/1592538959

If anyone's still following this thread, here's another great editorial piece by Highline/Huffington Post: 21st Century Gold Rush

From a print perspective, The Society of Publication Designers, SPD, and MagCulture showcase a lot of great work. I'd also check out NiemanLab and Poynter for articles about innovations in the industry.

Uh, yes please I work on 2 editorial products and this is insanely helpful. I ask for stuff like this in the slack channels I'm in constantly and I feel like I never get any response