I just finished watching the A&E set for the first time a couple of months ago. What a great ride.
I'd place Farscape in my top 5 sci-fi series for sure.
In regards to certain episodes people have mentioned already, I thought taking the stone was OK, The Locket was great, and I actually didn't mind A Perfect Murder. I had to go back and double-check afterwards "oh, and this is the one everyone hates?" and yes, it was. I liked the mind-bending use of partial reveals in the first third. It was not a GREAT episode though, no. It was merely OK.
I thought the biggest stumble in the series was the very end (last ten minutes) of season 3 and the beginning of season 4. There didn't really seem to be any reason for everyone to take off in separate directions. Or if there WAS some reason, I totally missed it. I've kind-of blocked the first three episodes of Season 4 out of my mind but I remember not liking them very much.
As has already been mentioned though it does right itself about halfway through the season and the conclusion was very good.
One other thing I will mention- the video quality in S4 takes a hit due to the episodes being in widescreen but having the same number of episodes per disc. People with the Starburst sets are lucky in this respect. I'm sure their S4 looks better than mine.