There are parts of each season that stand out:
In S1 the sequence of GGGoH, MoSB, PML, Witness, HiM and ASU are great. (Especially if you watch Witness where is was supposed to be.)
For S2, there are some individual good episodes such as ToGoM, SG, Phoenix, LL and TF but I don't care for the whole as much.
S3's strength lies in Lois and Clark coming to grips with who they are as a couple. I especially like WHaLtTA, OP, JSN, UW, HiWtHI and TA.
For S4 there are really only two sequences I like. The LoTF - BE end of the NK series and the PvLL - DLW set.

Overall, I picked S3 on the strength of all those personal relationship moments. In my opinion the strength of the first half of S3 overshadows the aargh sequence.

Bob