I will share my observations about my own sightings. Turning Japanese: In the mission where you go into Madame Geishas home, right before you go in look along the top of the walls behind it. Clan of the Cave Raccoon: In the mission where you take recon photos, he will be watching over the whole area from the small chunk of land at the top of the waterfall that is large and hard to miss. Of Mice and Mechs: In the very first mission, he will be on the building with the large clock. If anyone sees him in Go West Young Raccoon or the Saudi Arabia level (not Copycats), I would like to see him. I have also heard that he can be found in the first recon photo mission in Turning Japanese. I don't know why I obsess over finding him in all of the time periods in the game, but I have always wondered why he is robotic even though he is wandering around in prehistoric times. One last thing I'd like to point out is that your binocucom says you are being chased (glowing red, etc.) when you zoom in on him and he looks at you. I wish they would make DLC of fighting Clockwerk as each ancestor, like a seperate DLC missions for each level where the ancestor fights him. Possible starting with the oldest ancestor to the youngest ancestor in the game.
I saw him during the Pretty in Pinker mission and when you had to use Sly to scale the sinking ship during act 5. When i first saw him i blew it off as "What the hell is an Owl doing her in Japan....", then halfway through the game they were talking about time travel and it just hit me like O________O OMG THAT WAS CLOCKWERK.