Q: Do ARC Troopers (from the Clone Strike expansion) count as Clone Troopers for the purpose of Order 66?
A: Yes. An ARC Trooper is a special kind of clone trooper, even though the words "Clone Trooper" do not appear in its name.
Q: Can Emperor Palpatine (from Rebel Storm) include characters with Order 66 in his squad? The glossary definition for Order 66 says that the character can be in a squad with "Emperor Palpatine, Sith Lord," but I'm not sure if that should include any "Emperor Palpatine." For example, both couldn't be in the same squad because of the Unique restriction (their names are similar, obviously, with the exception of the phrase "Sith Lord"), but does this make them similar enough to both get this benefit?
A: No. The Order 66 glossary entry mentions a specific miniature by name. "Emperor Palpatine, Sith Lord" refers only to the character from the Revenge of the Sith set. If it were meant to apply to the Rebel Storm Palpatine, it would have said "Emperor Palpatine" (which would apply to both) instead.
Q: The commander effect for Emperor Palpatine, Sith Lord says that I can include characters with Order 66 in his squad. If the Emperor is defeated, what happens to any characters with Order 66 in the squad? Are they automatically removed from play? Do they change sides and start to fight for my opponent's squad?
A: Characters with Order 66 in Emperor Palpatine, Sith Lord's squad continue to fight for that squad normally even if Emperor Palpatine is defeated during the skirmish.