I say "Thank You!" because I (usually) genuinely appreciate the service they are providing for me, and I want to show them support in what I can only assume is a thankless and stressful job.

The caveat is I won't thank a rude customer service representative...because, in that scenario, I don't view them as deserving it.

Also, just because I thank a good employee for their service, that doesn't mean I have to lay it on really thick by saying, "Oh, I could learn a thing or two from you, you pro!"