Well, you might be in for a some confusion as season 2 has yet to be released on DVD. All the other seasons are (although seasons 3-5 are out of print).
Season one was the best season all around. Strong episodes and nice building of an overall story.
Season two, they changed gears. The first half of the season is very stand alone, save for a few minor arcs. It also features nearly every staple of sci-fi (time travel; alternate universes, etc). The latter half of the season starts to pick up again when they give us a strong story arc that caps off the season. The end of the season actually ends pretty strong.
Season three follows on this wave and I personally thought it was good. Not out of this world fantastic, but not terrible either. However, there is very
little arc development and it is mostly standalone.
Season four, I would argue, is on par with season one and it wrappes the series up in a nice package.
Then there is season five, which I have no idea what they were thinking. They should have just marketed it as a spin-off and be done with it.