The Naked Time (TOS) and Time Squared (TNG) both have elements of time travel involved.
, Alternate timeline episodes
, Parallel universe episodes
. There's a lot of these, will have to filter out the bad eggs.
And these don't even count the instances of "fake" time travel, e.g. that Hirogen holodeck simulation involving Nazis.
Time Squared is awesome -- I love time-loops! But I'm posting to see what appeals to others!