The readme contains an itemized comparison, though it sounds some of this actual comparison may be out of date or more specific to git-encrypt (yet another project) git-crypt does appear to use openssl libraries for example.
transcrypt is just a Bash script and does not require compilation
transcrypt uses OpenSSL's symmetric cipher routines rather then implementing its own crypto
transcrypt does not have to remain installed after the initial repository configuration
transcrypt generates a unique salt for each encrypted file
transcrypt uses safety checks to avoid clobbering or duplicating configuration data
transcrypt facilitates setting up additional clones as well as rekeying
transcrypt adds an alias git ls-crypt to list all encrypted files