Over at Jessica Faust's BookEnds blog, there's a raging debate about whether or not to thank the agent/editor for their time and consideration when submitting a query. Well, maybe not so raging -- it seems like Jessica is about the only one who says not to do so; commentors mostly disagree with her. Do you prefer to be thanked when agents (or writers, if you accept unsolicited slush) submit work? Or do you consider that unwarranted groveling?
I visited the links you provided. My first thought was, WHAT?!! Who's this doing query critiques? Who does she think she is, horning in on my territory? Wouldn't it be easier, instead of critiquing a query, to send her readers to EE's blog, where there are nearly 400 query critiques? Incredibly, Evil Editor isn't even among the blog links in her sidebar! That right there should send up a red flag.
Then I read the query critiques. They aren't even funny!!
But, getting to your question, I see nothing wrong with a simple Thank you, or Thank you for your time and consideration. I pay my masseuse, my psychiatrists, and my pool boy very well, but I still thank them for their services.
On the other hand, that stuff is usually at the end of the letter, and I've already made up my mind whether I'm interested before I get to it, so it isn't going to alter my decision.
If I were a writer, I would expect my agent to include a word of thanks when submitting my manuscript to a publisher. I can't recall receiving a letter from an agent who didn't do so. You shouldn't have to tell your agent that you want a thank you included with your submissions, but perhaps you do.
After critiquing 380+ queries on this blog, the phrase I'm sick and tired of reading is: I look forward to hearing from you. Of course you do. That's the whole point of a query letter. Is the agent more likely to get back to you if you declare that you look forward to it? Does she sort the slush into piles from authors who look forward to her response, and those who don't? I don't believe so.