In zsh, you can use a recursive glob:

mkdir ~/epubs
mv **/*.epub ~/epubs/

In bash ≥4, run shopt -s globstar (you can put this in your ~/.bashrc) then the command above. In ksh, run set -o globstar first.

With only POSIX tools, run find:

find . -name '*.epub' -exec mv {} ~/epubs \;

In zsh, you can use a recursive glob:

mkdir ~/epubs
mv -- **/*.epub ~/epubs/

In bash ≥4, run shopt -s globstar (you can put this in your ~/.bashrc) then the command above. In ksh, run set -o globstar first.

With only POSIX tools, run find:

find . -name '*.epub' -exec mv {} ~/epubs \;