I have a small 3 drawer plastic organizer on the counter. One drawer for primer, foundation, powder, blush, concealer, tinted moisturizer. One drawer for eyeshadow (including palettes) eyeliner, primer, mascara. One drawer for brushes, tools, perfume, lip gloss, lip balm, and lipstick.
I bought a knick knack shelf with several small cubbies in it (got it at good will for like $5). I hung it on the wall right by the sink in the master bath. It's not the most stylish but it works and we don't have any real decor in there anyway.. It also has enough space to hold my hair products too.
And then a I have a small set of plastic drawers under the sink that I store my other items that I don't use all the time in addition to samples and extras of stuff.
I wanted everything off the counter so I bought a hanging makeup bag that has four zippered containers on it. The bottom is big enough for my Naked palettes. It is cute and was $20 at Marshall's. It hangs on an over-the-door hook and I can easily put it away under the sink when I need to.
I have a cosmetic train case. Google this if you're not sure what it is. You can find them at every price point from $30 at target to a nicer one for $100+ at sephora.
I have a couple different types of organizers that I use inside my drawers
white plastic baskets ( organizes lipstick, eyeshadows, blushes, etc)
clear acrylic cup holders (organizes brushes, mascara, pencils)
the white plastic baskets I have in different sizes
The clear acrylic cup holders are regular cups - I bought these in the kitchen section of Target. You can also get these types of cups in the bathroom section