I have several favorites.
1795 held the lead for almost three years until I saw the first Laura story line. (1967) To me, it was the epitome of what DS might have become if it had retained its original, traditional soap plots and casually mingled them with supernatural elements. It blended the unexplained (mysterious, screaming portraits, unidentified, disappearing dead women) with more mundane problems (child custody battles, blackmail.) Also, it was original and creepy.
I also enjoy 1995 and 1897. 1995 was extremely atmospheric and suspenseful; though it was perhaps the shortest story line, I really do feel that it was one of the best. The 1897 story line, on the other hand, was the longest I think. Hence, there are many memorable characters, a variety of plot twists, and some incredible dialogue in its first half.
Getting back to 1795, it was well-written (much more exciting than the Barnabas-stalks-David plot, IMHO) and featured some nice acting. I thought that all of the players seemed rejuvenated in their new roles; they were so much fun to watch! Also, it marked the time when I truly became interested in the show as something more than background noise while I did my homework, so it's a favorite for sentimental as well as content/quality reasons.
My least favorite story lines are the 1970 Gerard & Daphne haunting, the current Dream Curse/ Adam & Eve shows, and 1841 parallel time. Boring, bad writing, blecch!
ProfStokes