I have a traincase, a massive one. It's been discontinued and it was made by sephora and was like $90 and it still doesn't hold all of my crap. they have other ones now (and in some nifty colors) and they're quite sturdy (much more so than the like $250 MAC traincases).
I started using palettes for my eyeshadows because it was really becoming too crazy and it's not too hard to depot most eyeshadows. Also if you bring in 6 remaining plastic containers from depotted MAC shadows you get a free eye shadow, lip glass or lip stick :3
I'm thinking of investing in a really nice vanity too... I have to wait and see on that though :|
In regards to keeping brushes straight, a nice glass pot for a potted plant filled with rice or small beads works well to stick em in (its a sort of, sephora inspired design).
I've been wanting to try this : www.youtube.com/watch (a brush easel..made out of toe spacers for when you paint your toenails).
He has a lot of great ideas for make up and other related things...like using this tool case as a make up bag, mwahahaha. www.youtube.com/watch I'm looking forward to getting one on my own :3

I have a ginormous (14x9x10) Kryolan case that's about half full of Kuchi jewellery and half makeup. I still haven't bothered coming up with a real system of organization, though - just stuff everything wherever it'll fit. :P

I love, love, love those clear plastic organisers that sit on a shelf for at home organising. On the go I have three different box wossnames. I usually use my traincase. I looked everywhere for one with battery powered makeup lights for those times when you have little light to get ready. I finally found one and it's bliss. It's lovely and huge and can carry everything. I also have a smaller caboodle thing which is flat and folds out with a little mirror that pops out.

I have an assortment from over the years. I have a couple of Caboodles, and some craft boxes from places like Jo-Anns and Hobby Lobby. I also have some ArtBoxes, but most of all I love tool boxes and tackle boxes. Definately shop around in the sports and hardware type stores before you make your final decision. I keep all my bindis in a 3 ring binder. I cut up some cereal boxes and used my three hole punch to put holes in them and put them in a zip binder. I also have some that I cut smaller and put in sheet protecters inside. Then I have an extra mirror and my spirit gum, super glue and eyelash adhesive in a pocket in the front. I used to have a little mini one from a makeup organizer (three ring binder that is), but I lost it at a show somewhere. I have seen them in office supply stores too, in the planner section.

My main kit I carry is a nice ArtBox, that I really should have waited and bought the same layout in a tackle box for about a 1/3 of the price. :)

TOOTHBRUSH HOLDERS!!!!!! (The cups with a top that has holes) For travel DIY the same idea with a yogurt cup an mini brushes.