Aesop use glass bottles and recyclable plastic pumps/parts.
Maria Nila use plastic, but claim they have climate compensated packaging (I think this means they plant new trees - it may not mean much to be fair - I haven't got a clue).
Kjaer Weis do refills for their makeup and use stainless steel.
Ilia and RMS beauty use glass and metal.
Tata Harper use glass and some plastic (for lids, for example).
EcoTools make brushes, and they're supposed to be pretty good. I think Superdrug and Boots sell them.
I am not entirely sure, but it seems to me that Paul and Joe makeup comes in cardboard packaging, and that you can buy refills for a lot of it, such as lipsticks. I don't know how much plastic there is in their packaging, so you'd have to check this yourself if it has any interest.
I'd also suggest a Z palette and then buying eyeshadow/blusher/powder in pans with magnets so all you have to replace is the empty metal pan. Loads of brands sell their products in pans (Mac, MakeupGeek come to mind). I don't know if that would work for you though.