I've been slowly loading my books, and have about 400 or so on my K3 now, with a couple hundred more to go.
I let Calibre send about 200 books to my Kindle last week and didn't notice any indexing slowdown -- but I did it before bed so I'd be ready for the weekend, so maybe that isn't a fair comparison.
My latest strategy is to pick a few collections, such as Lee Child's Reacher novels, send them to the Kindle, and immediately use Kindle Collection Manager to organize them into a collection. When an author (such as Karin Slaughter) has multiple collections, I've done this:
Karin Slaughter -- Will Trent/Atlanta series
Karin Slaughter -- Grant County series
My plan for now is to continue this sort of collection organization. I think that authors with a prolific output (such as Stephen King) will simply have their own collection with just the author's name as the collection title.
They can have my K3 when they pry it from my dead, cold fingers but I sure wish someone at Amazon would consider giving those of us who do have larger libraries choices on how to organize those libraries. No matter what kludge I use, it's still tough to scroll through and find what new book I'd like to read next.
I've mentioned this before, but I tend to go on buying sprees for my ebooks exactly as I used to do with pbooks. It's not uncommon for me to buy 8 or 10 books at a whack, then a few days later to buy a couple more. When I had a special shelf for unread pbooks, it was easy to peruse the cover art and/or the back cover description to remind me books waited for me. Now new books tend to get lost as I jump back and forth between new novels, old favorites, and of course medical reference books.