I've treated you all to a fair amount of doom over the past few weeks, so I feel I owe you a bit of sunshine every now and again. The truth is, you can (and should!) exercise a small amount of influence over the comp titles chosen for your book, and it begins relatively early in the process. That is, with (drumroll, please): the query letter.
If you read Nathan's blog (and who am I kidding? 99.9% of you are here because you do), you may know that when writing a nonfiction book proposal, you're expected to do market research, which partly entails (you guessed it) coming up with a list of previously published books that are similar to, but not quite just like, your book. Necessary for nonfiction, and, à mon avis, a great idea for fiction as well.
Caveat (there's always a caveat): if you choose to do this, be smart about it. Do not compare yourself to Dan Brown or any other mega-bestselling author. While it may be true that your new paranormal thriller has secret societies and child wizards in it, who's going to take you seriously if you write "Lost Symbol meets Harry Potter" in your query? No one, that's who. So do a lot of research, pick a couple of books that have been published in the last few years that are similar to your own, and only devote a small portion of the query to said books (remember, you're selling you, not somebody else. Vende te ipsum*, and all that). Of course, if your book is nonfiction, you can (and should) spend more time talking about potential comp titles and the similarities/differences between them and your book, as that's supposed to be part of the package.
And another thing: please, please, please resist the temptation to say (or even think, if you can help it) that your book is 100% unique and original, and nothing like it has ever been published in the history of publishing, because this is almost assuredly untrue. Yes, your book should stand out in some way from the crowd, but it's probably similar to a lot of other books already out there, and (counter-intuitive though it may seem) you actually stand a better chance of demonstrating the unique qualities of your book by explaining how it's similar to, but ultimately different from, the existing books in the genre, rather than coming off as ignorant/arrogant/what have you by insisting you've written something totally unlike anything that's ever been published.
Now, after all that, the upshot of including a well-chosen comp or two in your query is this: if and when you get an offer of representation, said comp(s) will already be floating around in your agent's brain when (s)he starts shopping your manuscript to editors. It's likely (s)he will mention said comp(s) when doing so (you can always ask him or her to do so if you feel strongly about it, though you may want to check the BookScan numbers beforehand). Now those comps are floating around in the editors' heads, meaning that if one of said editors acquires your book, those comps are already being talked about long before the book is ever sold in. With a little luck, those might be the very books the sales team uses as comps when they sell your book to the major account buyers.
So, in trademark Bullet-O-Vision™:
• Admittedly, you don't have a lot of direct influence over those pesky comp titles, but there are some things you can do: namely, include a couple of well-chosen comps in your query and spend the appropriate amount of time discussing them (less for fiction than for non-).
• Be smart about the comps you choose—don't go crazy comping yourself to mega-bestsellers and don't go around telling everyone you've got nothing to compare yourself to because your book is that groundbreaking.
• Don't be disappointed if they don't stick, but if they do, talk with your agent (once you've got one) about mentioning them to the editors they're shopping your MS to. Consider checking the BookScan numbers (your agent may be able to do this for you) to make sure you're not inadvertently shooting yourself in the foot.
• Whether or not the comps you prefer are used, it can't hurt to have your agent ask the publisher what titles are actually being used as comps. If you're sufficiently hands-on/neurotic, feel free to read these books, check their BookScan numbers, &c to get an idea of to what and to whom you're being compared.
• At the end of the day, your writing is your writing, and you're selling yourself and your book, not the guy next to you clutching his. Write well, work hard, and take advantage of any opportunities that come your way. And good luck!
*Not bad for a guy who never took Latin, no?