Agree with Out of Time's assessment that Kes' problem as a character was the ghettoization in Sickbay, essentially as a glorified Nurse Ogawa. The surprise on Janeway's face the one or two times she shows up on the bridge says it all...
In terms of good character moments, "Cold Fire" shows the beginning of her potential, as well as its possible dark side, and should really have been explored more. I also liked "Warlord", when she emancipates herself from Neelix (Lien's acting as the evil tyrant with the pixie face was cool) and "Darkling", when she falls for that alien vagabond type. "Before and After" is the obvious one.
But since NCC-1701 was looking for little Kes moments as well as major episodes -- "Parturition" is a nice one, when she deals with Neelix' jealousy and his fight with Tom; as is Investigations when she says goodbye as Tom heads out on his suicide mission. It's only a few seconds, but Lien packs in a fair bit of friendship wallop into her hug, without saying a word.
I disagree, though, with the posters who said Tom Paris' character stopped being interesting after Season 3, and that the Doc was the only one who got an arc in the series. Yes, Season 4 -- thanks no doubt to the arrival of 7/9 -- was a lull for Tom apart from the P/T relationship. Although in "Vis a Vis" he goes through an interesting bout of I've-stopped-being-a-bad-boy-now-what? depression. And then we have Season 5, with "Thirty Days," "Bride of Chaotica!" and "Gravity," and the post-demotion aftermath through Season 6 when he claws himself back up the rank ladder with some solid officer work and good leadership displays. It was Tom, not Harry, who designed and built the Delta Flyer, and Tom who took over the mission Chakotay botched in "One Small Step". He becomes a husband and a father in Season 7 ... all that from starting out as a Starfleet reject/convict with a chip on his shoulder. If that's not a character arc, I don't know what is.