When we praise someone, is it a way of showing we feel superior to them?

It could be, I've never really thought of it that way before, but I do think that it would depend on the person and their hidden intentions. I've never really used the phrases "well done" or "excellent work," then again I'm not a teacher or in a profession that normally uses those phrases. But those phrases do seem a little rehearsed to me. I do know that after I've read something that's nicely written (I love to read,) I normally lose my wits over it and say improper things such as, "holy cows, this is amazeballs," or, "LK;JF;LAKSJF;LSJDFASD OMG THIS IS AMAZING," at no time when I say that do I feel superior, just inspired. I've also noticed (back in high school) that a lot of my teachers would write long paragraphs about how amazed they were when it comes to my creative writing, but simply write "well-done," like you said, when it came to my academic writing (research papers, analytical papers, etc.) I've always been a lot better at creative writing than academic writing. I think (sometimes) that people put "well-done" because they really do think your work is decent, but not inspiring, or because they're just too lazy to write more than that. This is a really interesting question I've never thought about. 

Yes, in a way it is.

No. It is just a statement that someone did a good job.  Like praising a dog when it preformed a correct command.  Whether it be a math problem solved correctly or a kitchen cleaned very well, it was a good job, excellent work, well done.  An affirmation of praise.