Have you signed up for Zulily.com? I receive their emails every 2-3 days (I subscribed with a free gmail account to avoid cluttering my regular account). They run limited sales from a number of vendors for baby & childrens' clothing, clothes for mommy, toys, and other child gear. I think they have quite a few more vendors now than they used to-- it seems like there are a ton more on the page when I click over! Not all of these companies sell organic clothing, but usually at least a few do. Some really cute stuff, too!! I've seen both very simple, staple items as well as cutesy stuff.
Check it out! :-)
I second the happy green bee outlet suggestion.
Beyond that, you really have to shop the sales online. I'm on the mailing list for my favorite brands so that I know when things go on sale and when there are good promo codes (and I do stack sales and promo codes when possible). Some sites also offer special deals if you friend them on facebook.
Sage Creek Organic has a lot of stuff in their sale section (for younger kids) and they've got a 30% off promo code that expires tomorrow. Hess Natur has a 25% off promo through July 24 and there are a few things left in their sale section. I try to get Hanna Andersson stuff off eBay, but if there were an outlet store near me I'd go there and use coupons to keep the prices down.
I went with the thrift store option again - you can't beat 99 cents an outfit! I went for the plain, all-cotton stuff, even though I know not all cotton is, um, "healthy" cotton. I'm going to embroider a few designs onto them. DS picked out a few he likes, like a turtle and an elephant, and those shouldn't be too hard to do. I like to embroider. I also picked up a huge, and I mean huge bundle of all-wool vintage thread... It was $2 for the bag and they all had their original price tags (from, I think, the 70's? Or earlier?) - and they were all like $2 a piece back then. All in all, it was about 50 bundles of wool thread, and I can't imagine they wouldn't be more expensive today... So, score.
There are lots of t shirts (as well as shorts, hoodies, etc) at happy green bee that are "boy friendly" colors. You just have to look on page 3 or 4 (and beyond) in the clearance section.
But you will never, ever beat those thrift store prices!