My favorite episodes were:
"Catch a Falling Star": Sam leaps into a stage actor understudying a famous singer in a production of "Man of La Mancha" and discovers the piano teacher he had a crush on as a teenager is in the cast. The great John Cullum plays the famous singer, with Janine "Southern Exposure" Turner and Ernie "Pumbaa" Sambello also in the cast. Bonus: Scott Bakula sings! He was nominated for a Tony in 1987 for 'Romance Romance'.
"Shock Theater": A tour de force for Bakula as he leaps into a patient in a 1970s mental hospital who is being subjected to electric shock therapy. The shocks jolt him into other personalities he's leaped into, disrupting his memory of who he really is and threatening to sever his tie to Al and the project forever unless a way can be found to get his memory back. Bakula's acting is astonishing in this episode as he alternates between assuming the personalities of past leaps (including a woman and an old black man in the deep south) and freaking out because he doesn't remember who he is and he doesn't know why Al keeps trying to talk to him.
"MIA": The best Al-centric episode, which finds Sam involved with helping a woman named Beth who, Al reveals, was the one great love of his life. Al struggles with the reality that he can't change - that Beth gave up on him after he went missing in Vietnam and married someone else - and his desperate desire to change his history to one where he didn't become a miserable alcoholic after coming home to discover Beth was gone. Bonus: this episode has GREAT music!
Fun Fact: Don Bellisario was heavily involved in an early 1980s show called "Voyagers!", which involved a hapless time-traveler and his young companion who's a history whiz (the show was marketed to kids.) Part of the storyline in later episodes revolved around an 'evil Voyager' who was running around history messing things up, leaving the heroes to have to try and stop the damage. The concept is VERY similar to the 'evil leaper' and I'm sure Bellisario recycled the idea in QL.