To me all storylines were great in S4. First the mystery was the best after S1, it actually made sense and was creepy and we didn't know what the hell happened till the last episodes. It had a great last episode and the whole thing ended with the great last scene (girls saving Kath's secret) and the shocking 5 year jump. Katherine was also a great addition to the show and the fact she had history on Wisteria Lane made it even better. Susan and Mike were finally together, something we all wanted, Bree's fake pregnancy gave us some great comedy moments (the barbecue scene, Halloween birth giving
). Gaby/Carlos/Eddie provided some soap love triangle drama along with Victor. Lynette had her best season, battling cancer gave Felicity a chance to shine. So many emotional moments for her. Then there's the peak of the season, tornado and it's aftermath, I still get shivers when I remember that episode and the follow up, again Lynette had the biggest moments there. Then Kayle goes psycho on Lynette. Also Lynette's mother appeared. Wow, thinking about stuff that happened in this season make me realize how great it was even more, have to watch it soon again.
I think the strike actually contributed to making this season so good. It had 17 episodes, less filler and more quality.
Also the ratings went up, show was back in top 5 most watched in that tv season and was No1 scripted show for the first time, beating CSI.