Wow. Well, this is a big question.
1) English card sets are arranged numerically. With sets that have 1st edition forms, I typically notebook them side by side. For example: Card 1 1st Edition, Card 1. Card 2 1st Edition, Card 2. Etc. Shadowless Base Set is an exception. Those cards are notebooked seperately. For cards with reverse foils I typically put them in front of their standard prints. Addtional prints of a card, for example the "fractured foil" versions that were typically included with 3 packs are at the end of the set from which they originated. Currently I have notebooked Base Set through Plasma Freeze. I haven't gone out and bought new notebooks and sleeves in a while, so Plasma Blast through Roaring Skies are currently in standard card boxes numerically arranged. Once I actually buy the notebooks and sleeves they will be notebooked as well.
2) Rare misprints and stamped cards (Prerelease, Prof. Program, States, Regionals, Cons, etc) are currently in a seperate notebook. Currently, I have 20 of my rarest stamped cards on display in a frame. Eventually, most will be displayed in this manner.
3) Theme Deck coins are also notebooked using the same kinds of sleeves used for managing mint coin collections.
4) Pokémon marbles are currently displayed in a giant pokéball display.
5) Plushes are kept in my daughters room for the most part.
6) Tomy figures are currently stored in various rubbermaid tubs.
7) Oversized Vinyl Figures are on shelves throughout my house. These include Palkia, Giratina, Reshiram, and Zekrom.
8) Artifacts from my Top 14 position from the Emerald Brain Battle tournament are framed and displayed in my bedroom. This includes the certificate I received from the tournament, the Rayqauza T-shirt I got for competing, the letter I got from Nintendo of America verfiying my attendence, newpaper clippings associated with it, and photos. I also have the copy of Pokémon Box and the Pikachu Game Boy Advance SP I got as prizes on a shelf. I also have 2 Rayquaza promotional standees from the event.
9) A complete set of unopened Burger King toys from the 1st Movie are in storage with the Tomy figures, as well as several opened ones.
10) All of the badges, patches, etc I have earned from Pokémon Leagues from 1999 to present are shadowboxed.
There's probably more.. you get the idea. I have too much stuff. To give you an idea, these are some pics I took of my collection 5 years ago... Like last image shows, most of my collection is boxed and in storage.