There were some fun eps in s5. The Must Watch For Gay Slashiness Sub-Almost-Text Episode is "The Shrine". You must watch it if only to get context for half of the footage in recent SGA vids. I also quite liked "The Deadalus Variations" for parallel universe-ing, and "Remnants" was an interesting mindfuck ep.

On the other hand, if you are in the mood to watch something that will make your eyes bleed, try "The Inquisition".

I think "Doppelganger" was in season 4, that's definitely on my Best Eps list for the John/Rodney with bonus Sheppard doppelcest.

I fully support your goals of weird crossover OT4ness.