Both Martin Gardner (The Annotated Alice) and Roger Lancelyn Green have written footnotes to Alice in Wonderland and Through the Looking Glass. Here are some other authors who have written books based on Alice in Wonderland or/and Through the Looking Glass.
Alice Through the Needle's Eye by Gilbert Adair where Alice travels through the alphabet.
The Looking Glass War by Frank Beddor-a supposed 'true story' based on the two books, casting characters in the two books in different roles.
Alice's Journey Beyond the Moon by R J Carter. Alice goes into space, again with characters from the other two books.
Alice in Quantumland by Robert Gilmore. An allegory with Alice exploring the quantum world.
Automated Alice by Jeff Noon. Alice travels to a Manchester city in the future.
A New Alice in the Old Wonderland by Anna Matllack Richards. Written in 1895, it concerns an American girl visiting Wonderland.
Otherland, four books by Tad Williams, based on Wonderland
The Thursday Next novels by Jasper Fforde also refer to Wonderland characters, especially the Cheshire Cat.