PokeDolls are one of the most popular items among collectors. They were first available in 2002 in Pokemon Centers in Japan. They are known for being a chibi version of the Pokemon, and the Japanese tags have a small drawing of the Pokemon on it. Earlier versions have the red Pikachu tag. Some are even available in larger sizes, called Delux PokeDolls, or DX Pokedolls for short.
More on DX PokeDolls: DX Pokedoll - Pokemon Collectors Wiki
Banpresto makes a wide variety of Pokemon plushes and figures, and most of it is easy to get because of its availability. They also make MPC's, short for "My Pokemon Collection" of just about every Pokemon in existence! They also make holiday plushes and other assortments of promotions, such as the I Love Eevee one shown here. More specifics of Banpresto merchandise can be found further down.
Takara Tomy makes a very wide selection of merchandise for Pokemon fans, ranging from plush, to watches, to figures, to keychains! The plush tags also feature a small drawing of the Pokemon, but are not similar to PokeDolls. They also produced the talking Pokemon plushes.
Jakks is the company that makes most of the Pokemon merchandise you will find in America, it's often distributed in popular stores such as Toys R Us, WalMart and Target. However, they are known for having horrible distribution habits, some things not coming out until months after they were supposed to, and other things being ridiculously hard to find.
Nintendo World Plush/Figures
Nintendo World, located in New York City in the United States, features a Pokemon Center on its first floor with PokeDolls, plush and figures that are the same as the Japanese ones with English tags. They also have shirts, which are pictured further down in the clothing section. They are the same plush that are found in the vending machines as well as at Epcot.
Canvas plush are small plush that are only available in stores at the Pokemon Center in Japan. They are in lighter pastel shades, meant to look like a painting. Their tag includes a Smeargle with a small painting of the Pokemon. They are available in a wide selection of Pokemon.
Clearfiles are collectable folders with human characters or Pokemon on them, often done for promotions. They are 8 x 10 inches, and are a usable folder to keep papers in if you wanted to! They are made of thin, bendable plastic, not paper.
Pokemon Kid figures are another very popular and affordable piece of merchandise. They are produced by Bandai and are available in just about every Pokemon you can think of, some even in different attack poses. There are also clear variations of some of them, as well as larger ones. There have even been some kid figures produced of human characters, including Ash, Misty, Brock, Gary, Jessie, James (both in their white and black uniforms), Nurse Joy, Officer Jenny, Professor Oak, Cilan and Iris. They come in a small box along with a sticker and a piece of candy.
More examples of kid figures can be found here: http://toys.qee.jp/menu.htm#POKEMON
Zukans are small figures that are on a 1/40th scale of the Pokemon's height. They are known among collectors for being very detailed. In Japan, they are distributed in gashapon machines. More recently, Tomy Yujin Europe have started to sell these figures, under the title of 'Evolution Figures'.
More on Zukans
Pokémon Zukan figures - Bulbapedia, the community-driven Pokémon encyclopedia
Clipping figures are very small figures produced by Bandai, known for being in cute and dynamic poses to look as if they were "clipped" from a scene. Similar to kid figures, they come with a card.
Museum figures are produced by Banpresto and are known for being in dynamic poses and being very detailed. The figure itself is separated from the base in which it sits upon. Some of the older ones are very rare, difficult and find and valuable now.
Pokémon Trading Figure Game - Bulbapedia, the community-driven Pokémon encyclopedia
Pokemon Trading Figure Game figures are meant to be used for a two player game. The figures themselves are available in Kanto gym leaders, as well as many Pokemon. The human ones especially have fetched very high prices among collectors, and the Groundbreaker series, because it was never released, are very rare and hard to come by, as well as being often sought after by collectors.
More information can be found here: Pokémon Trading Figure Game - Bulbapedia, the community-driven Pokémon encyclopedia
Not to be confused with the Trading Figure Game figures, Trading Card Game figures were found in promotional tins for the Trading Card Games. They are also often in dynamic, interesting poses.
More can be found here: TCG Figures - Sealed Chamber
Straps are exactly what they sound like, they are small straps that can be attached as keychains to pretty much anything. They are available in lots of different forms, and are only available in Japan but most are very common and very affordable. Some can only be acquired by winning through the movie lottery at 7-11 in Japan. There was also a promotion on Pepsi bottles in Japan in which small straps were attached to the bottles of Pepsi.
Stamps are another piece of merchandise that are available far and wide in many shapes and sizes, most commonly the base sets that are released. They are exactly what they sound like, most being a figure on top of an ink stamp.
Charms are also available in all sorts of shapes and sizes. In 2012, the Pokemon Center did a promotion in which they released charms of all 651 Pokemon to date. So there really is merch for every
Pokemon! The charms are often in different poses, and many have a back and front.
Chou Get Figures
Produced by Bandai, Chou gets are small figures on a peg that can be bought from Gashapon machines in Japan. The bases are interlocking so that you can connect them to other Chou figures!
There is an enormous amount of different Pokemon apparel available in countries all over the world! In America, Pokemon shirts can be found in Hot Topic, Toys R Us and Nintendo World. At Nintendo World, they are usually in youth sizes so they will not fit most adults. In Japanese Pokemon Centers, they have a much broader selection with lots of cute and fun designs, however, they are also mostly in youth sizes.
Pokemon are featured on a large amount of food products in Japan, from milk, to noodles, gum, and bread, and some food products come with Pokemon stickers and cards inside.
Credit for images:
Jo The Marten
And many Google image searches. If you see one of your images here and would like credit, please contact me and I will add you in and I apologize!