Wow. There are Pokemon as Wikipedia entries?!? I guess I shouldn't be surprised, given the nature of Wikipedia, but I never knew that... it's actually kind of creepy...

Actually, I have read (and contributed to) a guide on GameFAQs on this very subject. I don't remember if Lugia's name was explained, but on my last check Latios and Latias have not yet been explained. Those two are confusing indeed...

Anyway, paraphrased from the aforementioned guide I have this to offer:

Kyogre: Even though it looks like something about an ogre, that part of the name is apparently a play on the word "orca", the killer whale. "Ky" is spelled "Kai" in Kyogre's Japanese name, Kaiorga, and I have heard "kai" equated with "lord", or "god". Therefore, Kyogre's name would mean "whale god", or something of the sort. However, according to my Japanese dictionary, "kai" means "shellfish", giving "shellfish whale", but that doesn't make sense. Oh, well.

Groudon: This one's easier. The "grou" obviously comes from ground. The "don" part is a Spanish title of respect or esteem (such as one might see in Don Juan or Don Diego). It more or less means "lord" as well, giving "ground lord". "Don" might also be from the ancient Greek for "tooth", like in Iguanodon "iguana tooth", and, well, Groudon's pretty toothy, too.

Rayquaza: Until I heard it pronounced in that really weird Destiny Deoxys movie, I thought it was "Ray-KA-zaa", and so I got the impression of the Aztec god Quetzalcoatl ("KET-zaal-ko-AH-tull"), who is often represented by a feathered or flying serpent. This might be part of the case, but I know now that the name is pronounced "ray-KWAY-zaa", and so it is more likely that the "quaza" part comes from quazar, having to do with celestial bodies. Either way, "rey" is Spanish for "king", giving either "celestial king" or "flying serpent king". Pick whichever you like.

Deoxys: On that note about Destiny Deoxys, Deoxys's name comes from the term "deoxyribo neucleic acid"- commonly shortened to DNA. This is part of why its tentacle-arm things are shown twisted in a double helix.

Growlithe/Arcanine: The first part of Growlithe's name is obviously "growl", a very annoying noise that dogs tend to make when they're miffed at you and five seconds away from rending your flesh. The "lithe" part looks like it comes from the word "lithe", quick and limber, and Growlithe is a pretty fast Pokemon, but on hearing the pronunciation ("GRAU-lith", not "grau-LAITH") you might realize that it is more likely to have come from the highly combustible metal element lithium. Again, the "canine" part of Arcanine is obvious, and the "ar" sounds a little bit like the bark of a dog, but it probably also stems from the word "arson".

Rhyhorn/Rhydon: Most of this is obvious, with the plays on the words "rhinoceros" and horn. Again you have "don", or "lord", with Rhydon's name. But interestingly, "rhy" was not just used as a bastardized spelling of "rhi". Those are also the first three letters of "rhyolite", a very hard volcanic rock (and Rhydon lives in magma).

And, as another note, Feraligatr's name could also stem from "ferocious", not just "feral". But feral works too.

Those are just some of the more interesting ones I can remember. You might want to go look at the GameFAQs guide (I'm too lazy to find the link, but it's called "Name Guide" and is under the FireRed/LeafGreen section, if nowhere else in the Pokemon sections) for some interesting piece by piece explanations of the names. Really, I've been meaning to ask the author to add the names of some of the more significant trainers, too... I mean, ones like Lt. Surge and Misty are pretty obvious, but not everyone might recognize Sabrina, Giovanni, Lorelei and Falkner, and even I'm still not sure where Koga, Tate & Liza and some others came from. Those are possible things to discuss here, too. I'd add the ones I know, but not right now because I've already mentioned I'm lazy. Whatever. Outta here.