What parts of Bitcoin (litecoin etc) are Little Endian?
All numeric values on the wire are little-endian with the exception of network addresses and ports, which are big-endian.  This includes Sha-256 digests which are treated as 32-byte numbers.  It does not include data pushed on to the script stack, however, which is copied as-is from the script element.

The regular numbers aren't really a problem since you end up shifting the bytes to form the internal numeric value in either case.  But the 32-byte values are expensive since you end up allocating a new byte array to reverse the bytes as you go to/from the wire protocol byte stream.