At Target: Look for Sonia Kashuk brush sets. These make great gifts and they are often packed in attractive kits. Target also has some great cosmetic bags. I was there earlier in the week and saw gift sets consisting of three different sizes of matching bags. Look for those in the cosmetic department.
For stocking stuffers, Target has tons of Hello Kitty, Karma, and Bonne Bell items, plus they have quite a few holiday cosmetics sets.
In the purse section, you can find some really nice, yet affordable handbags. Consider buying one and filling it with random cosmetic items!
At CVS: Look for Essence of Beauty Brushes. These are good value brushes and mixing and matching some would make for a great gift. CVS also exclusively carries Skin Effects and Lumene products. Both are great lines for creating a custom made facial or skin care set.
At Walgreens: Look up front for a great selection of fragrances and bath products. They seem to have more than many of the other stores this year.