The Avro Canada Jetliner is another example, though it never went into production, and if you are including the Tu-144 then the Concorde belongs as well, and the original 737 also had its engines mounted directly under the wing, without pylons. While it is not quite the same, I think all trijets except the DC10/MD80 had the third engine buried in the tail.

There were many military designs, such as the British V-bombers, with engines mounted in or directly on the wing, without pylons.

Hrm, I thought the Sud Aviation Caravelle also lacked them, but I was wrong (though they're in an unusual place on it).