I'll pick a favorite from each season:
Season 1 - "Get Houston" (I have a lot of favorites in this season, including "Deadly Fashion," "Here's Another Fine Mess," "The Yacht Club Murders," "Whose Party is it Anyway?," "A Deadly Parlay," "Fear for Tomorrow," and "The Hunted")
Season 2 - Tie between "Love You to Death," "China Doll," "The Monster," and "The Secret Admirer."
Season 3 - "Apostle of Death"
I've been recently re-watching the series with adult eyes. The last time I saw these episodes was between the ages of 10 and 13 for first-run and 14/15 for syndication. I'm 41 now. When I was young, I wanted Houston and C.J. to get together. Watching the series now, I see that the first season is the best in this regard. She and he were very equal, were great friends, and had some sexual tension between them. Season 2 was the beginning of the end for C.J. The producers, directors, and writers basically started taking her out of this equal partnership and kept her at the office more. They basically gave the character a tranquilizer and dropped the anvil of Buddy Ebsen on her in the third season. At the same time, they turned Houston into an obnoxiously macho womanizer. To me, this ruined the show along with extricating a lot of the humor from the first season and turning it into a "serious" run-of-the-mill, action-packed detective drama. How many times can a man get a major blow to the head before he is permanently hobbled or killed, I ask you? They gave up character development for action and removed the humor. Sad. I still enjoy it through my childhood eyes, thankfully, but had I been an adult when I saw this first-run, I would have yelled at the television to tell C.J. to get the hell out of there before it was too late; and that she was prettier and smarter than his ocean of bimbos, and basically solved all of the mysteries and deserved better than Houston.