Well, there is always the trap of mistaking "my view" for "everyone's view", but I personally find Thanks very helpful. Like many users, I use it to indicate gratitude for a helpful edit and to let people know that I'm interested and supportive of their efforts.
In some contexts, I also use it to say, "I saw your reply to my comment". I don't think this is a misuse. It's not materially different from the brief "Thanks" that one says in person, when someone hands you something that you wanted while you're busy (or they are). In person it looks like this: I'm talking to someone while walking down the hallway in one direction; you're hurrying down the hallway in another direction. You have something that I need. As we approach, you hand it to me. I say "thanks" as we hand it off, and we both keep going. On wiki it looks like this: I'm doing my work, and you're doing your work. You have some piece of information that I need. You post it; I see it. I click the thanks button so that you know that I've got the information now. We both keep going. It's the same thing, just translated to my wiki life rather than my meatspace life.
I have rarely heard of uses that give me pause, e.g., someone being Thanked for posting a patently rude message or for joining an edit war, but in the few cases where I've bothered to check the log for the names of people Thanking someone, I suspect that those Thanks were truly genuine expressions of gratitude and support.