Tough one. I think you need to take a bit of the person's likes/dislikes and personality into account. If the person was willing to watch 3 episodes, I'd say the first two and then a third one, as the Elements of Harmony episodes do give a good background to all of the characters, making later scenarios involving them make more of an impact. That being said, they aren't the single best episodes that showcase all the goodness that is pony either.
However, with only two, let me see. My recommendations:
The episodes that converted 2 of my friends:
- Dragonshy: If the person likes adventurey, dragony stuff. Some funny scenes. Also has a nice Charlie's Angel's parody in there.
- Swarm of the Century: A variety of funny scenes. Pinkie Pie being Pinkie Pie.
Other good ones:
- Bridle Gossip: MAYBE. The obvious "Don't judge a book by it's cover" message might be a turn-off, but the poison joke makes for some hilarious moments. This might be better with more of a background on the ponies, however, since knowing their personalities might make the poison joke pranks funnier.
- Winter Wrap Up: If the person in question is a fan of songs, since the song in this episode is reason enough to watch it. If they aren't, then I'd probably avoid it for now.
- The first two (Friendship is Magic): Even though I said above that they aren't the best, they are still pretty good. It has elements of adventure, an evil villain, and introduces all of the ponies. Ideally, it'd be better to start with these and then show a really great episode to bring it home, but even without a third, they aren't too bad. They are the ones I started with and they managed to hook me just fine
- Sonic Rainboom: This might just be my bias talking, but this is a pretty awesome episode
. The only danger is that it perhaps is too centered on Rainbow Dash and her dream. For me that's a good thing, but for new ponies, it might be too much of a pony they just got introduced to.
- Applebuck Season: Hehehe...sleep deprived Applejack is silly
. Funny stuff here. The danger is the same as the above episode, too much of one pony.
- Best Night Ever: Again, the song. You get to see some hilarious scenes with all of the ponies. The danger to this one is that it would probably be better to have a decent background on the mane six to get more of an impact when the night goes sour. It'd make Fluttershy's part especially a lot more humorous if you knew her character.
- Any CMC themed episode: Now don't get me wrong, I personally love the little tykes and find them rather adorable and funny (Obviously, considering Scoots is my avatar). That being said, a lot of people find them annoying and they can especially turn off a potential new convert. I hate to say it, but it's true.
- Suited for Success: Another one that I love, but an episode centering on making dresses carries the danger of leaving a sour taste in a non-brony's mouth. Too much of a "girly" concept to start with.