As a native Japanese speaker (who played the first two games in Japanese), I feel compelled to point out the following:
Nidos
It is often thought that the "nido" comes from Cnidocyte (which anybody who's taken Bio 2 should know). "Ran" in Japanese can mean "orchard." I also feel the "rhino" thing is a little dubious, as in Japan the word for rhinoceros is sai. But then again, I don't have a better alternative so who knows.
Golduck
I just want to point out that the "gold" thing may be because psychic stuff in Pokemon is often symbolized with gold, like the Gold Badge (Japanese Marsh Badge).
Gyarados
Almost definitely not "gyre" (Gyarados is his original Japanese name). May be from gyakusatsu (mass slaughter), and dosu (onomatopoeia for puncturing, probably flesh in this case).
Lapras
While he is based off the Loch Ness monster, the name is probably from either lapis lazuli or Laplace.
Mew/Mewtwo
Doubtful it's from the cat noise, as "mew" is not an onomatopoeia for cats in Japan. Possibly from mutant.
That's all I got for now.