Inner Light is certainly a popular choice. I tend to prefer more unique, higher concept episodes. Cause and Effect is thus a favorite of mine too, but
Yeah, Timescape is tops for me. I like the concept and especially the clever play on landscape. One of my favorite titles of anything, if that can be a thing.
Props for mentioning Time's Arrow, definitely an underrated episode in general.
The other one I'll throw out (probably my 2nd favorite) I haven't seen mentioned yet is The First Duty. Before Enterprise (I think) came out, one rumor was it would be a Starfleet Academy series. This episode really shows you what could've been, but sadly wasn't. Still think it would kick ass.
DS9 is the best Trek series by a wide margin IMHO.