1. Below the Root by Zilpha Keatley Snyder. This series is out of print, but it is probably available from your local library. A fabulous fantasy series set in a different world, with sinister secrets just, well, below the root.
2, 3, and 4. The rest of the Time Quartet. Cheating a bit here, but they are three separate books, after all. I promise not to pick any more L'Engle books though. :) They are A Wind in the Door, A Swiftly Tilting Planet, and Many Waters. Each of these books deals with the Murray family, continuing their story and adventures in time and space.
5. The Giver by Lois Lowry. I don't know if I associate these books because they were my favorites growing up or what, but for some reason I feel like if you liked A Wrinkle in Time you'll like this one. And its sequels, Gathering Blue and Messenger, of course. I hear there is also a fourth one coming out, which I'm very excited about.
6. When You Reach Me by Rebecca Stead. Of course I have to have this one on the list. Stead uses A Wrinkle in Time as something of a muse, having her main character Miranda read the book over and over and borrowing the time travel theme.
7. The Wee Free Men by Terry Pratchett. Not exactly the same idea and the writing style is a bit different, more quirky and whimsical, but it has great charm and a fascinating world. Of course, if you've read any Discworld novels, you know what I'm talking about.
8, 9, 10 (and 11). The Dark Is Rising sequence by Susan Cooper. Yes, a bit more cheating, but again, four separate books! Another fantasy series with plenty of old charm akin to the L'Engle books, staring with Over Sea, Under Stone and continuing with the book the series is named after. There are four books in all, and the borrow heavily from Welsh mythology. Very fun, with a rich setting and great world building.
There you are! If you have any more to add to this list, please feel free to mention them in the comments. If I haven't read them, I'll be sure to seek them out!
Also, if you're interested, I made this short video celebrating the 50th anniversary of A Wrinkle in Time.