I would agree with previous comments that saying nothing would be the best way. Or, as others have also suggested, compliment your friend when you think she looks good. Maybe, if she wears something you don't think looks good on her, you could say something along the lines of "I tell you what, (insert whatever you have in mind) would go with that and look really good".
Ultimately, if someone likes, and feels comfortable wearing, certain items of clothing, it's really their business alone. But I do understand your concerns as her friend and your dilemma.
As for others commenting, maybe you could show loyalty to your friend by telling those making the critical comments that it's up to her what she wears, and they should either tell her to her face or just keep their remarks to themselves.