I have one: Mew is (as far as I know) the only Pokemon with real-world whereabouts.
Remember the diary in Cinnabar Mansion?
The explorers were searching locations in
Guyana.
Also, Lt. Surge is a foreigner... his nickname is The Lightning American, remember? I guess he's based on Guile or something.
One that everyone should know is that the regions in the Pokemon games are based on areas of Japan. Kanto is based on... well, Kanto, Johto is based on Kansai, Hoenn is based on Kyushu... possible somewhere as specific as Kagoshima.. and Sinnoh is based on Hokkaido. There isn't anywhere in Japan like Orre, and I'm unfamiliar with the territories from the Mystery Dungeon and Ranger games.
In one of the early episodes of the anime, Misty is scared by a Caterpie, and Ash says, "A cow? Where?!", while in a black and white dairy cow costume. This is because the Japanese words for bug and cow (mushi and ushi, respectively) sound similar. In a later episode, Ash is seen eating gyudon, a dish almost always made with beef (gyudon could be translated as 'beef bowl').
Now, some interesting questions. Slowpoke supposedly evolves into Slowbro when a Shellder clamps onto its tail... so why can Slowpoke evolve when there are no Shellders around? Similarly, what's up with Magneton and Dugtrio? Why do they count as one Pokemon, and not three? I guess I can understand Magneton, but a Dugtrio is just three Digletts in the same hole!
I can understand most type match-ups. Water and grass can erode rocks, a great fighter is useless if someone uses telekinesis on them, and birds eat bugs... but what exactly does steel have on rock? Why should the dark fear bugs? I don't really understand what it is rocks do to ice...