Over the last year, I've replaced (and expanded) my library of programming books from physical copies to ebooks. In each book, I have a host of bookmarks. Unfortunately, I didn't save them in one front-to-back read through so my bookmark lists are all out of page order. Is there a way to sort/organize them by page number?
There is simply no way to do this as of iOS 6 and iBooks 3.x.
Apple is amazingly quiet about bookmarks in iBooks - other then mentioning that it is possible. If you follow this link to the iBook FAQ, click "iBook Features", then "Can I bookmark and save my page?", you will notice that they mention it is possible to bookmark pages, but don't even mention how to view the bookmarks - let alone an alternate way to sort them. About the only other iBook information page I could find was this with no information that was pertinent to you.
On the other hand, the Kindle iOS app seems to prefer ordering bookmarks by page number instead of date. It might be painstaking, and I'm not even sure it would transfer you bookmarks over (in which case it would be worthless), but I do know it is possible to email books and PDFs to Kindle for reading (see "Read Personal Documents:" in the above link). It may be possible to sync the books to your computer, and then email them over.
Honestly, what you're asking for doesn't seem to be a very popular request, so it may be a very long time - if ever - before Apple releases such a feature.
I also tried searching for a variety of general terms to see if it would pull up a list of bookmarks - in page order, but even that failed.