Dragon Roots Magazine, which if you haven't heard of yet you can check out at
www.dragonroots.net, is a bit torn on this subject.
When I started writing this magazine, I did so because WOTC took away the printed versions of Dragon and Dungeon. I secluded myself from the net while getting it started and I found out about 4e about 24 hours before the big announcement. So, for me, 4e was a hit right where it hurt.
I was left trying to figure out if I wanted 3.5 content or 4e content. I am still on the fence, but it appears most people want 4e content so Dragon Roots will follow suit and produce 4e content.
That said, I know that a lot of people are going to resist change and I am normally one of those people. So Dragon Roots will also produce 3.5 material as well. I personally have a lot of articles that I wrote for Dragon, but never submitted, that contain 3.5 material. They will make their way into those pages in the future.
To make a long story short, if we get some 3.5 articles, we will print them, just like we will print 4e material. It will start to be mostly 4e material, but I could see a 3.5 section or even one or two issues dedicated to 3.5.
The good thing about writing a magazine is that the material printed can usually be converted easily and also the ideas generally span more than the current version. A lot of the things people write, like campaign building articles, is good solid advice that any DM or PC can make use of regardless of what version they play.