The Transformers in Japan were all numbered - usually C- followed by a number or D- followed by a number. C represents Cybertrons (Autobots), D represents Destrons (Decepticons). In the first series, there were no prefix letters, instead the Autobots were released as 01-15 and the Decepticons were 16-24. After that, the 2 factions were integrated until number 50 where the 2 factions were split into C- and D-. The numbering system went a little weird as of the 4th series: Masterforce, it is presumed that Takara started skipping numbers in order to start each new series with a round number.
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The list on this site is by order of release, starting with 1 though to the last release TF-10. Each character's Japanese name is listed first with their Western name listed in brackets if there is a difference.

Therefore:
D-201: Blood (Bomb-Burst)
means that the toy's number was Decepticon 201, it's Japanese name is Blood but it is known as Bomb-Burst in the West.
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A lot of name differences are not actually differences in the name, but rather pronunciation. A good example is Swoop, who is commonly believed to be known as Swarp in Japan, however he is actually called Swoop in Japan too. Japanese pronunciation of English can be awkward at times due to sounds that do not occur in Japanese, resulting in mistakes like this. It should be noted that the reverse is true as Japanese is regularly mispronounced and/or bastardised into English (Deszarus into Deathsaurus for example). Notes are included on each individual page.
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Certain Western characters were not universally released in Japan. Ratchet, Dirge, Cosmos, Warpath, Gnaw, Squalktalk, Beastbox and Repugnus were only available by mail-order, while Sunstreaker and Skids were only available in a giftset. Reflector, who was available by mail-order only in the US was a regular release in Japan. Megatron was never released in Japan with all of his gun extension parts until the reissue in 2000.
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Gears, Whirl, Roadbuster, Omega Supreme, Jetfire, Topspin, Twin Twist, Barrage, Chopshop, Ransack, Venom, Sky Lynx, Runabout, Runamuck, Targetmaster Hotrod, Targetmaster Kup, Targetmaster Blurr, Targetmaster Cyclonus, Targetmaster Scourge, Backstreet, Dogfight, Override, Chainclaw, Catilla, Groundbreaker, Splashdown, Sky High, Gunrunner, Quickmix, Scoop, Landfill, Grandslam, Raindance, Needlenose, Spinister, Quake, Crankcase, Ruckus, Windsweeper, Bugly, Finback, Iguanus, Carnivac, Snarler, Roadgrabber, Skyhammer, Roadblock, Vroom, Bludgeon, Stranglehold, Octopunch, Doubleheader, Pincher, Longtooth, Actionmasters and some Micromasters were never released in Japan in any form.