Well, there is the all-favorite 'dig 3 blocks down and cap off the entrance' technique, but I assume you know about that.
What iI like to do is make a 3x3 hole 2 deep. Then...
I dig some more... diagram in need.
: 1 block deep
%# : 1 block deep
% : 2 blocks deep
!
! : door
% % #
% % #!
% % #
% % #
% % #!
% % #
works nice. It's able to fit a chest, crafting table, furnace, and a bed, although you may need to build into the wall.
