Automated Alice is very good, very weird. I wouldn't recommend The Looking-Glass Wars if you are a very dedicated fan, because they might anger you. The author is a bit smug, and quite dismissive of Carroll's work.
Exeunt Alice is very good, and is written so that you could almost believe Lewis Carroll wrote it.
And while it is not an actual sequel, try Pandora Hearts, a brilliant Manga heavily based on the Alice books.
A New Alice in the Old Wonderland is also good, and contains many Tenniel-esque illustrations by the author's daughter (Hey! That rhymes!).
Otherland Volume One: City of Golden Shadow features some scenes in a virtual world based on Through the Looking-Glass.
Jasper Fforde's Thursday Next series contains some Wonderland characters, including the Cheshire Cat, the Red Queen, the Court of Hearts and the Bellman from Hunting of the Snark.
Fantastic Alice is an anthology of short stories based on the Alice books. Some are quite good, though a few are quite mediocre.
Also, I am going to try these books very shortly:
- Night of the Jabberwock
The Wonderland Gambit Trilogy
Lewis Carroll: a Biography