Fawkes hung around for a while until the end of the main storyline
Spoiler
I fired him after waking up in the Citadel, because it seemed like an appropriate time
and he said I could find him at the Museum of History, outside the entrance to the Underground. But, I've checked there several times and he's nowhere to be found. Where did he go?
Dogmeat's a little weird, I didn't even know about the bow-wow-buddy until the Dogmeat's Puppies perk opened up (which I took) and then I found the junkyard. We were great friends until
Spoiler
the aliens abducted me, and apparently killed Dogmeat, because that's the notification I received shortly after being buttprobed
and when I got back down to the Wasteland, there were no puppies outside 101. How come?