The Titans have historically left their creations as guardians in each of their important sites. The Earthen in Uldaman, who are the ancestors of all the modern-day Dwarven clans, the Tol'vir in Uldum, who were mostly likely tasked to keep watch over both the Halls of Origination and the imprisoned C'thun in the neighboring Ahn'Qiraj, and a large number of Earthen and Mechagnomes as well as the Watchers in Ulduar.
Mogu'shan Vaults is an interesting case though. It contains a number of Titan artifacts, one of the engines which were used in their reshaping of the world as well as a forge akin to the one in the Halls of Stone, used to pump out a large number of Mogu Simulacra warriors... who look identical to the "real" ones. The Titans have historically made their landmarks fit the environment that they are created in, so if the Mogu didn't remodel the structures to suit their tastes, it may have been built as such by the Titans, which the Mogu would then use as the base for their own architecture.
So, there's two real possibilities here. The Mogu are creations of the Titans, who upon their departure, turned against their instruction and used the relics they left behind to forge an empire, or the Mogu stumbled upon the Titan artifacts in Kun-Lai purely by chance, and tampered with them for their own ends.
We know that the Sha are the remains of the old god Y'shaarj, in some sense. We don't know much about him, if he is in fact the unified form of every old god, whose death split him into other powerful beings, or if he was just one who was killed and cursed Pandaria, but he was worshiped by one of the ancient insect kingdoms, as the Quiraji did with C'thun and the Nerubians did with Yogg'Saron. There are titan facilities near each of the known old gods, and even when we face them in-game, it doesn't actually keep them down for long. C'thun's been active behind the scenes since his defeat, empowering Cho'gall to assist the Twilight's Hammer to bring about the Cataclysm (and there were some plans for a return to Ahn'Qiraj in Cataclysm that never came to be). Yogg'Saron might also be somewhat active, if the Puzzle Box ends up being a little more than just a toy.