Season four was ENT's most consistent season I thought. I enjoyed the multi-part storylines they did. Most were good, if not great with the Vulcan trilogy being my favorite.
My picks for worst:
Storm Front I-it failed to carry the momentum generated by the last six episodes of season three. I didn't have a problem with the Alien Nazi cliffhanger but Coto did so very little interesting with it opting instead to go for a very dull and formulaic first hour that improved slightly in the second half. It was like Manny didn't even try.
The atmosphere was poor, the sets felt like sets which stood out and the whole time travel explanation was poorly explained and was too confusing.
Divergence-Affliction was a strong first hour but this conclusion was a major disappoint failing to capitalize on the threads in interesting ways. Section 31 looked inept and the whole rationalization for working with the Klingons I didn't buy Under scrutiny it falls apart.
Hernandez was wasted, the action was stale in the last acts, Trip returns to ENT too quickly in one of the more disappointing resets.
I did enjoy the sequence in the first act, I loved the clever explanation of why the Klingons had smooth heads and the reordering of neural patterns explained the more sophisticated Klingons we saw on TOS.
Bound-just silly. The Orions lacked the sultriness and viciousness of 60s beauties like Yvonne Craig. They looked fake and trashy. I thought the humor at the end was forced. I didn't care for T/T it felt forced as well. The story was pointless.
I left out TATV because while seriously flawed I don't find it the abomination most do. It isn't the worst ENT episode nor is it the worst Trek episode ever. There are plenty worse. Despite its shortcomings there are enough elements for me to give it a pass in this contest-the numerous well done character moments(Archer/T'Pol in Trip's quarters, Archer/T'Pol at the end, Trip/T'Pol in the shuttle, Riker/Trip at the end), the recreation of the 1701-D sets and the ship itself, and seeing two of my favorite Trek characters(Riker/Troi). I also appreciated the idea if not the execution Brannon came up with for the finale--bringing closure to the 1987-2005 era of Trek by incorporating TNG characters observing a holoprogram of the ENT crew.
I am one of the few that don't mind Riker and Troi being in the episode (sorry folks, TNG is my favorite Trek series and I will never complain if I see more of it). However, IMO they should have had a post-Nemesis Riker and Troi appear (those sets were obviously not from the Enterprise D, the story doesn't fit in with the TNG episode Pegasus, etc). Here is how I voted:
Of course I do appreciate the fact that it was refering to the Organians which we'll later see in TOS.
And Manny Coto was making Enterprise so enjoyable- it ended too soon. And of course, Trip dies. 
