I thoroughly enjoyed the adventures with S'Daru (hope I got the name right) and the aliens who implanted the humans in the Philippines. The last one I ran...and man were the players freaked out...half of them wanted to hole up in the sticks somewhere and wait for what they thought was the inevitable alien invasion.....
I also ran Black Madonna once with some supernatural elements, such as basically making what was left of the Jansa Gora be a sort of dimensional gate with Filpiowicz being something of a magically enhanced fellow who could soak up a lot of bullets...but he wasn't un-killable.(I was running Twilight 2000 as a alternate world in the GURPS 4th ed Infinite Worlds milleu, sadly, that part floundered..it seemed many of the group was very anti-military (NYC at the height of the Iraq war). Also, there were dimension hopping Nazis who made a deal with the scumbag brute in SSD-1109 (His name escapes me at the moment) and they kill off the rest of the team for a chance to grab the Madonna for themselves.