For reasons I can’t quite explain many publishers don’t sell direct. My guess is that for single issues it is a no profit game and you run the risk of angering Diamond and local shops. That is a risk most publishers don’t want to take. What you are left with is a lot of the more “indie” or “lit” publishers having the webstores because they won’t ever steal enough traffic from shops to anger anyone and they don’t do a lot of singles. I know Top Shelf (www.TopShelfComix.com), Fantagraphics (www.Fantagraphics.com), Drawn & Quarterly (www.DrawnAndQuarterly.com), No Brow (www.NoBrow.net), Secret Acres does their own stuff and Koyama Press stuff in the U.S. (www.SecretAcres.com), Archaia (www.Archaia.com), I am sure there are a ton more I am forgetting.
I know Avatar Press sells through this site though I am not really sure what it is- (http://www.comcav.com/cart/index.php?main_page=index&cPath=1). Dark Horse owns www.TFAW.com so that is sort of their store, although not very BigCartel-y.