I agree with a lot of what JohnnySoprano said.
Season 1 is still my favorite. The Pilot, College, Isabella, I dream of Jeannie Cusamano, and Pax Soprana are all top notch episodes in my mind. episodes like Boca, 46 long, and Meadowlands are just a notch below. This season is great at finding a balance between the two families and the amount of airtime given to each one. Classic TV.
Season 2 is next for me. Again, great episodes this season from beginning to end. I like this season more and more as i re-watch it. Early on this wasn't one of my favorite seasons but it has climbed the ladder. From where to eternity and Knight in white satin armor are amazing eps. Funhouse is a very thorough and entertaining season finale (i love the music montage at the end).
Season 4-After seasons 1 and 2 its hard for me to put them in to order but i'll give season 4 the nod over 3 and 5. Great opener BTW. I did NOT like the Carmella-Furio love story but the rest of the season is solid. I really liked the work of Joey Pants in this season. Chris's drug habits and Junior's trial also made for interesting moments. Bobby starts to become more of a focal point in the series. They show a different side of the mob. Not as many great eps. as 1 and 2, but a solid season overall.
Season 3- This series drops in rank IMO because of a rather weak (relatively) opener and finale. They just didn't do it for me. Pine Barrens, To save us all from satans power, and others were good episodes. I just didn't buy Jackie Jr. as a main storyline. Also i was very disinterested in Meadow's relationships. Again there were some standout eps. that will go down in Soprano history, but as a whole the seaosn wasn't one of the top one to me.
Season 5- Now most people who I've talked to love this season. Not me. I didn't hate it by any means but i didn't love it either. This is last to me as of now. Like season 2 though, it could change in time.
With season 5 i wasn't crazy about the Tony B storyline. Okay we get it, Tony's love for Tony B stems from feelings of insecurity and basically selfishness. This was no great revelation for me. I got sick and tired of Tony and Carm's separation after a while. I DID like some of the Melfi scenes, Johnny Sac becomming boss, the tension with NY, and the resolution of Adrianna's role. In the end though i think Tony was as unlikeable in this season as any and that hurt it IMO. And, again, the separation and Tony B storylines that i wasn't thrilled about. Still great TV, better than anything else on, but not my favorite when comparing it to other Soprano seasons. I won't call it worst but least favorite. Let me say though that Long Term Parking, Test Dream, and Irregular Around the Margins were very good eps.
I'll wait for season 6 to finish before i rank that, but i think it will end up being one of my favorites. Probably up there with 1 and 2.