In the Pokemon franchise, there are a lot of materials which fall under a specific catagory. While this can be a bit overloading in some catagories, there is a something which some catagories have to easier tell the difference between all the materials. This "something" is color-coding, and in the Pokemon franchise there are plenty of things to color code.

Elemental Types:
There are currently 17 Type. Each Type has its own color which fits the element that Type represents. The colors are very importent (at least to the fan community) because they aren't only used to decipher Type, but also used for Gym Leaders, Elite Four, and possibly the Champion. Simply put, whatever Type that Gym Leader/Elite Four/Champion uses, that Type color would be the color that Gym Leader Name would be in (Example: Brock would be in Brown because he's a Rock-type Gym Leader). This rule also goes for the Gym that Gym Leader is in control of, but not for that Gym's city/town which will still be in Black (Pewter Gym would be in Brown, but Pewter City would be in Black). For Champions that don't have a specific type (Blue/Silver/Cynthia), their names are simply in Black.
I'll be splitting the Types by what Move Catagory (Physical and Special, which have no color-code and so will be in Black) they are in. The type ??? does not have a specific color as of yet, being listed as Black and Aqua.

Physical:
Normal - Grey
Fighting - Red
Flying - Light Purple
Poison - Purple
Ground - Tan
Rock - Brown
Bug - Olive Green
Ghost - Dark Purple
Steel - Light Gray
Special:
Fire - Orange
Water - Blue
Grass - Green
Electric - Yellow
Psychic - Pink
Ice - Light Blue
Dragon - Dark Blue
Dark - Dark Brown

Contest Conditions:
With the introduction of Pokemon Contests, each move has been given 1of 5 Conditions. Each Condition has been given its own color, and a Pokeblock (Generation III) or Poffin (Generation IV) of that color will increase that Condition by a certain amount depending the quality of the Pokeblock/Poffin.

Cool - Red
Beauty - Blue
Cute - Pink
Smart - Green
Tough - Yellow

Generations:
There has been so far 4 Pokemon Generations. Though many may refer to a certain Generation by what region it intoduced, it is not the exact way that Generation is represented. The appropriate way to tell what Generation you're talking about is by saying "Generation" and the the number that Generation is in roman numerals. It is not well known, but these Generations are also given a color.
For simplicity purposes, I'll also include what region that Generation introduced after the Generation but before its color.

Generation I - Kanto - Red
Generation II - Johto - Green
Generation III - Hoenn - Blue
Geneation IV - Sinnoh - Yellow

Pokedex Color:
There are many ways the Pokedex catagorizes a Pokemon, and one way is Color. Now I won't be listing what Pokemon is listed in what Color (If you would like to, Bulbapedia has an article for it HERE), I'll just be giving a general anylisis of what types can be found in that Color.
Strangely enough, orange is not a Color, rather Pokemon that are mostly orange are either listed in Red or Brown.
This list takes account of only the most seen Color for that Pokemon, it doesn't count their Shiny forms. In addition, if that Pokemon has multiple forms that are different Colors then the first form Color you're likely to see in the game is where that Pokemon is listed.

Red - Plenty of Fire and Bug; there is also a good amount of Water and Rock.
Blue - Watar galore; with Dragon and Ice filling up a nice amount too.
Green - Fertile with Grass; Poison also grows nicely here.
Yellow - Festive with Electric; having Bug and Fire celebrating here as well.
Purple - Ghost claim this home; neighboring them is a quantity of Poison.
Pink - Normal run free here; hovering over them is a few Psychic.
Brown - Normal and Ground has taken over; but Fire, Rock, and Fighting have taken a stand.
Black - Void filled with Dark.
Gray - Rock and Steel have structured; Ground also used for support.
White - Normal wander around here; also strolling is Ice and Psychic.

Main Series Games:
To finish this blog off, we'll end with the Main Series Games. Ever since the Game Boy, the Pokemon Main Series Games have always been on a Nintendo handheld. With each new Nintendo handheld a new Generation of Pokemon has been released and becomes a signature title for that Nintendo handheld.
Each Generation adds at least 3 Main Series Games. It begins with the release of 2 Versions, only slightly different from the other, then a 3rd Version is released having new features and plot the last two didn't include. Generation III is the only exception, as it included Remakes of the first two Generation I Versions.
Every Main Series Game has a Version name, and with that a color is assigned to it.

Generation I:
Red - Red
Blue - Blue
Green - Olive Green (Japan Only)
Yellow - Yellow
Generation II:
Gold - Yellowish Orange
Silver - Gray
Crystal - Light Blue
Generation III:
Ruby - Dark Brown
Sapphire - Dark Blue
FireRed - Orange
LeafGreen - Green
Emerald - Dark Green
Generation IV:
Diamond - Ghost Blue
Pearl - Light Pink
Platinum - Dark Gray

NOTE: If there is a Pokemon Feature that you think there is a color-code for and I didn't include, please leave a comment informing what feature this is. If there is indeed a color-code for this feature and is unrelated to the other color-codes above, I will list it down and give you credit for it.