Ideomancer has been around for a while now, and publishing gorgeous web-formatted fiction, as well as encouraging writers to mess around with narrative structures and formatting, including hypertext documents:
Ideomancer publishes speculative fiction and poetry that explores the edges of ideas; stories that subvert, refute and push the limits. We want unique pieces from authors willing to explore non-traditional narratives and take chances with tone, structure and execution, balance ideas and character, emotion and ruthlessness.
They accept fiction up to 7000 words, and have specific periods during the year when they accept submissions, so do please check before submitting.
Their home page: http://www.ideomancer.com/
Submission information is at: http://www.ideomancer.com/?page_id=20