I ask because I have several physical books that I would love to have digital copies of.

Most of the services out there are destructive, so you lose the book when you send it in to scan. I'm fine with this in theory, except for the fact that I'd hate to lose the physical book and have it replaced with a crappy digital copy. I've not had terribly great luck with my own attempts at OCR with documents (but I'm also not a professional).

Additionally, some of the books I want to scan have extensive footnotes. The ideal would be that the book gets scanned and edited to have these footnotes hyperlinked in the resulting ebook, but I don't know if anyone offers that kind of service. I'd even be okay with the footnotes just being eliminated if it's too much trouble. What I don't want is them just being flowed into the main text of the document.

There are a lot of different options out there, and I'm more than willing to pay for a good job. Has anyone used one of these services and can speak to their quality?

A while ago there was a post comparing e-books and hard copies. After chatting with a few people, I was convinced to spend the money on a Kindle to replace reading on my laptop.
It's an amazing difference and I'd recommend it to anyone who reads on a "normal" screen. My eyes don't get tired, night reading is more comfortable, I've got 40 books in my pocket, the screen really is glare free, and I've charged it once in a week and a half.
So if you read e-books, get a reader with the e-ink screen. It's worth it, and thanks to those who convinced me.