The wonderful online science fiction magazine Alien Skin has just published its final issue. They’ve been around for eight years and personally I was lucky enough to have a Fibonacci poem and a flash-fiction story (Time of Death) published by them. Understandably, running a magazine takes a lot of effort and the publishers are off to focus on other endeavours. As a paying market, they certainly would attract lots of submissions.
There are still some other online science fiction publishers to try with your short stories and flash. Some of my favourites include:
Duotrope also provide a fantastic searchable database of publishers, so take a look there for more publishers.