Now, I consider myself somewhat of a conaisseur of CSI. Basically aside from the last... like... 3 episodes in each series, I've seen every one.
My favorite episodes from Las Vegas are from the first season - the one with the teenage rave (the teen acting gave and absoltuely amazing and tear-jerking performance - really that's the main reason it's one of my favorites... the plot is about average, but it's that final scene with the teen that makes the episode) and then "Slaughterhouse" - the quadruple homicide with the 2 daughters surviving. The ending of that one left myself and my roommate staring at the screen for a few seconds before we both turned to each other with just a "What!? Did... did she just say? NO WAY! WOW!"
As well, I like LV's episodes from this season involving the car chase and with 4 dead gang members, a shot football star and a dead cop. Very good episode, lots of great performances there.
From Miami, I'd say that *their* quadruple homicide was a VERY good episode. One of my favorites. As well, "Kill Zone", the sniper episode was a very good episode. "Nailed" was a great one too... had me squirming for a bit when the episode started with the flashback of Ryan and Delko driving to the hospital. (This was the episode where the estranged ex-wife was found dead on the ex-husband's porch with nails in her from a nailgun). "Broken" and it's extra episodes involving the same sex-offender were terrific episodes.
Add in "Lost Son", first episode of season 3, killing off a CSI member, that was an intense episode.
"Under Suspicion", where Horatio is a suspect was a pretty good episode as well.
I love Horatio and his compassion for those he is involved with. Plus my roomy and I just get quite psyched up when he get a chance to start shooting... I love the backstory on him and how he gets to use his old skils every so often (bomb squad and acually having been trained in firing his weapon - he's like a freakin' sniper with that thing!)
And New York - I'm reading the episode briefs to refamiliarize myself and I'm just thinking of how many terrific episodes and cases there have been.
Episode 1 - "Blink" - They find 3 young women dead with only 1 "witness" left, who can only communicate through blinking. Absolutely horrifying and an amazing episode to watch.
Episode 9 - "Officer Blue" - A mounted officer is shot in a park with the bullet having lodged in his mount. The team has to wait to remove it until after the family who donated the horse in memory of their own slain officer (father/husband) says goodbye to Officer Blue.
Episode 10 - "Night Mother" - This episode sends chills down my back just thinking about it. Very, very creepy and amazingly acted episode. A sleepwalker is found overtop of a dead woman's body and the whole sequence has to be solved. Very dark episode.
Episode 14 - "Blood, Sweat and Tears" - A Romeo and Juliet type of case. Very good plot and a great bit of acting.
Episode 16 - "Hush" - A dead longshoreman is found at an unrelated crime scene. The team has to track the man's body (half of it actually) through how it got there and then to the crime that was really committed. As well, Aiden and Danny have to investigate a crime that leads them into a wierd world of S&M games.
And then Episodes 18, 19, 20, 21 and 23 are all very well done stories... I just don't want to write them all out here

In all honesty, I like New York the best... it's just a lot grittier and slightly more "traditional" in the methods they use to solve the crimes. Requires a little bit less "suspension of disbelief" than Las Vegas. Plus, Flack is probably my favorite character of any of the CSIs' cast members. Though, truth be told, the lead detectives in all the CSIs are some of my favorites. But Flack takes the cake - he's funny, he's your stereotypical "New York cop" when he's serious, and he just is cast very well.
Anyways, I've rambled on enough... time for bed.