For dugtrio, trio means a group of three, like dodrio, but in the description it says "Spanish word for three."
Murkrow is right for murky and crow, but there is also murder, which is a group of crows as well as death, keeping the dark element to it.
Forretress could also mean fortress, turret, and forest.
Clamperl has clam, pearl, but also possibly clamp, to signify that Clamperl slams its shell shut tightly.
The Bi in bidoof and bibarel could mean a prefix of "two," referencing their two buck teeth.
Happiny might also mean happen as well as happy, considering the basic evolution Chansey means odds. Blissey could also mean bliss and bless, to bring great happiness and good fortune, creating a trio of happen, chance, and bless, along with happiness and bliss.
Caterpie is right on the caterpillar part, but I think it might also be combined with "cutie pie," a term of endearment or of something adorable, possibly referencing its big eyes or just all around "cuteness."
I always thought that pidgey was a combination of pigeon and pudgy, like in that one episode, pidgeotto was pigeon and "auto"-pilot, for flying, and pidgeot was pigeon and pilot.
Rampardos could also have rampage, referencing that it tears things down easily with violence. I also agree with a previous user of rampart.
There is also other users that mention victreebel (tree) dragonite (knight) and sunkern/sunflora (sunflower, not just sun).
I'm probably talking out of the back of my head, but that's what I have to contribute. Sorry for the slight wall of text.