After watching and rewatching and rewatching, etc etc etc this series more times than I can count, I've come down to a simple system for ordering good vs bad episodes and that comes down to what I still watch and ones that I avoid. Season three though might be my favorite
The watchers
Evolution (Wesley creates a new race. ho hum just another day in the life of the Wonder Boy and Stubbs can be quite annoying but I like this episode regardless)
The Best Of Both Worlds Part 1 (classic)
The Offspring (I should hate this one but I don't. I guess I'm just a big softy)
Sins Of The Father (I'm a fan of all of the Worf episodes in the discommendation theme. Probably my favorite series spanning story arc)
The Most Toys (goofy at times, but I like it)
The Survivors (I wish they had done some follow up regarding the Douwd race)
The Defector (You gotta feel for Admiral Jarok)
Deja Q (refreshing twist instead of the usual all powerful Q)
Hollow Pursuits (fun episode, if a bit goofy)
Allegiance
Tin Man
A Matter Of Perspective (The various POVs are fascinating and I just like how the hearing unfolds)
The Ensigns Of Command (c'mon, admit it. you LOVED the look on Gosheven's face when Data blew up the pumping station. Suck on it, Goshy, suck on it

)
The Hunted (Super soldier badassery that can even fool Data)
The Price (Kinda have a love/hate thing going on with this one. I've always liked it but these days I fast forward through the Lloyd Braun/Troi romance scenes)
The Vengeance Factor
The High Ground
Transfigurations
The avoiders
Captain's Holiday (I'd rather have jamaharon than watch this one again but who wouldn't?

)
The Enemy (a little too Enemy Mine for my tastes)
Sarek (don't have anything specific against this one I just don't ever need to see it again)
Menage A Troi (shoot me now)
Who Watches The Watchers (never liked this one. However, it's been years since I've seen it and I'm due to revisit it)
The Bonding (boring)
Yesterday's Enterprise (good episode but I've seen it enough times)
Booby Trap (used to be a must watch for me but I've gotten tired of it and Picard, Mr archaeology wannabe, blowing up an unique artifact irritates me to no end)