Of the series leads:
1. Picard: Someone once said that Picard best embodied the ideals of the Federation among the captains (this was the 90s) but I still thinks that applies. He's a man of science, diplomacy, and action (but usually as a last resort). I also enjoyed the TNG crew the most. I have a nostalgic attachment to them and TNG, despite my misgivings at the no interpersonal conflict edict on TNG.
2. Kirk: Bold and charismatic, he was an inspiring leader. I mean who else could inspire his crew to break the law to go to the Genesis Planet and beyond?
3. Sisko: I liked Sisko's humanity, his toughness but also his vulnerability. And I liked how he was family man; really the only captain that had a relatively stable family life. Arguably the greatest warrior among the captains, though Kirk is also up there as well.
4. Janeway: During Voyager's run I never really got Janeway. She seemed way too inconsistent for me. But over the years I've come to respect Mulgrew's performance more. Still not a big fan, but looking at what faced Janeway, she got almost everyone home so I will give her that.
5. Archer: The weakest captain for me. I didn't start to get into the character into Season 3. I think he improved as a character an leader in the show's final two seasons, but still didn't quite come together for me. I still don't think his accolades were earned, more a deal of telling and not enough showing.
Of the guests, ones that stood out to me:
-Geordi LaForge: One of my favorite parts of "Timeless". I wish they would make it canon.
-Silva LaForge: I always liked Madge Sinclair so it was great seeing her again. I wish we had gotten a novel or comic (one of the Captain's Tables perhaps) giving us one of her adventures.
-Sulu: Really liked seeing him in "Undiscovered Country" and wished he had gotten his own series or a miniseries. It's cool that we've got some novels and comics though.
-Jellico: I liked how he was a hard ass. And he was right on Troi having a uniform. And his suspicions about the Cardassians were correct, though his approach was a bit too cavalier.
-NuPike: Just had the gravitas. Someone I wouldn't mind watching in his own movie or series.
-Original Pike: I like NuPike more, but I would've liked to have seen more of the original Pike. He seemed a bit more morose figure and might not have been as fun as Kirk but still I was intrigued by "The Cage".
-Garrett: Brief glimpse at a cool character in "Yesterday's Enterprise".
-Ransom: I really liked "Equinox" and how that crew was kind of a dark mirror of Voyager.
-Robau: More so for the visual than from what I actually saw in action. He just looked like he might have been a bad ass, and I would've liked to have seen him and George Kirk and crew on more adventures. Get on it Trek comics.
-Terrell: It was neat seeing him in "Wrath of Khan" and seeing him pop up in comics.
-Scott: I wish they had revisited Tryla Scott at some point after "Conspiracy". I liked the idea of her becoming the youngest captain in Starfleet.
-Hernandez: I liked her on Enterprise. I liked her relationship with Archer. Unfortunately the series was canceled and I can assume we would've seen more of her in later seasons. At least Trek Lit. picked up her story and gave her closure.
From Trek Lit.
-Calhoun: I really loved New Frontier when it started though I've lost interest over the years. That being said, Calhoun was a breath of fresh air, a bold, funny, charismatic, and kick ass character.
-Harriman: Yes, he's a canon character, but I've liked him better in the novels and comics. Also in the fan film "Of Gods and Men."
-Wong: Also, she's a canon character, but I liked her in the comic one-shot.