TCP/UDP/IP are BE, but that's largely an artifact of the time they were invented (when the LE/BE split was more even), hence networking hardware is probably where BE is still commonplace.

Most application protocols I've worked with are LE; serialisations like Avro, BSON, capnproto, protobufs, etc. come to mind, as well as numerous other proprietary ones. ASN.1 is a notable exception, but it's also much older.

But even though the protocols are big endian, is it generally the case that you always make the data itself big endian? (Asking out of ignorance, not rhetorically or sarcastically.)

It's up to the programmer. In the systems I've worked on, we always sent the data itself in little endian.