There doesn't seem to be any recent thread for the similarities between pokemon and real organisms, so as a biology dorkus I thought perhaps I could start a fresh one.
Most animal and plant-like pokemon do have a specific, intended real-world basis. Those that don't are often still similar to real species by sheer coincidence. Feel free to speculate, share knowledge, and leave any questions you might have on the subject; chances are good that if you're not sure what a pokemon is meant to be, I can probably find a real equivalent for you.
Here's just a few favorites of mine:
TRUBBISH - XENOPHYOPHORES
I often see people complain that Trubbish and Garbodor aren't "believable" as living creatures; that there's no way they can buy a blob of garbage being alive.
The thing is, living blobs of garbage do exist. I doubt anyone at Gamefreak was even aware of this, but actual organisms called Xenophyophores work pretty much exactly like the trash pokemon. Here's what one looks like:
What you're seeing here is sand, dirt, minerals, tiny fragments of seashell, hardened mucus and a whole lot of poop, all held together by invisible, branching strands of living slime. It's actually a type of huge amoeba, which collects inedible detritus - literally garbage - to form this protective coral-like body as it grows on the sea floor.
SHUCKLE - Scale Insects
This is pretty much my own theory, so again, not necessarily official, but certainly possible. Shuckle, as you may know, is a rather bizarre bug type hiding in a tough, pot-like shell, which produces delicious, nourishing potions as a by-product of its feeding habits.
In the real world, scale insects are tiny creatures related to aphids, who hide inside of immobile, secreted shells, and produce a sugary liquid called honeydew as they consume plant juices. Many other animals love the stuff, especially ants, who will "milk" these insects of honeydew and guard over them.
"Duh, a cricket, right?" Wrong! Despite being a "cricket" pokemon, this little guy's physical design is based on a beetle, the violin beetle!
These are pretty popular insects in Japan; they show up as monsters in several other series, and you can catch them in animal crossing! The real ones don't make noise, but they do secrete a paralyzing poison.
PHIONE & MANAPHY
These little guys are actually based on a type of swimming sea slug often known as a "sea angel," scientifically known as Clione. They're widely beloved in Japan, often drawn as baby-like blue creatures with antennae and fins.
It's too bad, when designing Manaphy, that they forgot the very coolest part; sea angels are predatory, and feed on other mollusks with a ring of barbed tentacles that shoot out of their faces: