I have several favorites, my top ones are the following:
Mega Kangaskhan. The concept is great, the child can finally fight alongside the mother. Design-wise, it isn't too different from regular Kangaskhan aside from the child being able to fight on its own, but it doesn't matter. This thing has one of the coolest abilities ever and it helped me in several of the lines at the Battle Maison. It is so powerful that it is almost ridiculous, but not in a bad way.
Mega Mewtwo Y. I think it looks a lot better than regular Mewtwo, the way its tail sticks out if its head is so cool. It also levitates which suits a Psychic-type. That high Special Attack is nothing to laugh at either.
Mega Mawile. I was already a fan of regular Mawile and this, plus the Fairy-type it gained in Gen 6, made it stick out even more. This is one case where two heads are clearly better than one, and where two fangs hits twice as hard. Huge Power is awesome too.
Mega Medicham. Regular Medicham is one Pokemon I have previously had a hard time caring for. It had a quirk back in the ancient days of Gen 3 where it had a higher Attack stat than Slaking, but I didn't really care for it apart from that. That didn't really change during generations 4-5 either despite Medicham becoming better with powerful High Jump Kicks and stuff. But then I decided to use Mega Medicham on my post-game team in X during this generation and I started to love it. The Attack and Speed boosts it gains upon Mega Evolving are great, it keeps Pure Power and it had a vast movepool to start with, so how come I never realized its awesomeness before? I guess the Mega is what really sold me on it. I also think its Mega design is fantastic, it adds a bit more mystery to this fighter.
Mega Manectric. I was unsure about this at first. Intimidate is cool, but at the cost of losing Lightningrod? I later learned that it wasn't that much of a loss since it can simply absorb Electric moves first and then Mega Evolve for some extreme power boosts. It also has a cool design and it helped me get my longest streak ever at the Battle Maison. Plus I was already a big fan of regular Manectric to start with and this did not change that for the worse, only for the better.
Honorable mentions: Alakazam, Gyarados, Ampharos, Tyranitar and Lucario. I should mention that there are several Megas that I have never used in battle so I don't really have a real opinion on all of them when it comes to my own experience of using them, this list might have looked different if I had tried all of them properly but now I haven't.