I still occasionally think about the series on Rome, and also the Rise of the Khans series. (Also, apparently, it's pronounced Jenghis - who knew?!). The series on World War I is also phenomenally interesting and really paints the picture of just how brutal and senseless that war was. The section on Verdun is particularly harrowing.
Another one that I think everyone should hear is "Logical Insanity", where Dan talks through the civilian bombing campaigns of WWII. He makes a case that the nuclear bombing of Hiroshima and Nagasaki fit into this wider pattern of bombings in a really interesting way - those two events obviously loom large in our thinking about history, but in the context of WWII they were almost... mundane. Just two more bombings of civilians in a war that was full of the same. (Dan makes the case in a much more fleshed out way, so please don't take my half-assed description as an indicator of the quality of the episode).
These have all fallen behind the paywall at this point but they are well worth the money and time.