I recommend the Mark Twain Library editions published by Univ. of
California. They're not exactly cheap, but they are attractive and
include the original illustrations, which are a must. The series
also has some volumes that come from manuscript material, such
as the "Mysterious Stanger Manuscripts."

This past year I used the Library of America volumes, especially
the two collections of stories, essays, etc. I don't think I'll
do that again, since I found the physical books rather dispiriting
to read: they're so solid and reliable and proper, and so lacking
in illustrations.

There are also some Mark Twain works in the Norton Critical editions.
These are nice because they have supporting material and a selection
of critical articles all nicely contained for limited projects
involving secondary material.

The Dover Dollar editions (some of which cost two dollars) also
include some Twain, but I've never looked at those to see how
textually reliable they are. They certainly are cheap, however.

Finally, you should get your library to acquire the recent Oxford
Mark Twain, which is relatively inexpensive (for a library) and
reliable and furnished with introductions and other stuff by
both academics and normal people.

GJ