I'm not sure how well Dragon Roots is selling, but it's one small press alternative that I know of. And it's actually
in print, which would put it ahead of 'Dragon', or what has become of that, at least to me and quite a few other gamers.
Paizo is continuing to put out very high quality products for 3.5. . . and soon for their own tweaked version of that ruleset, the Pathfinder RPG.
There are some smaller publishers still releasing material for it too, some of it also worth looking at, IMO.
4e hasn't really killed 3e, let alone any other system. And I doubt that it will.
Anyway, regarding Dragon magazine, there's Kobold Quarterly, as well. From their website's front page: "the spiritual successor to DRAGON Magazine" -- Erik Mona, DRAGON Magazine Editor. Sounds alright, eh?