As far as fanservice goes, there's a right way, and a wrong way of doing things.
The right way doesn't ultimately affect how the show is written. Rather than taking a fan idea and basing something around it, the writers take their idea, and add an element that both the peripheral fans and the regular fans would understand. For instance, in "Feeling Pinkie Keen", it could have been (and was originally) any random pony that dropped all that stuff on Twilight. By instead making it Derpy, they added an extra joke that the bronies would understand, without affecting the regular viewers. Another way to do this properly is to make a reference that makes sense without knowing it's a reference, such as Rarity's wings evaporating; it makes sense regardless of whether or not you know the story of Icarus.
Have a scene that needs a DJ? Use DJ Pon-3
Need a klutz? Use Derpy
The wrong way is to focus on things the bronies would understand, but the regular fans wouldn't. For example: an episode about Rainbow Dash coming out of the closet; shippers would crap themselves, but the kids watching would just go "huh?".
In a nutshell:
Good fanservice: Kids and adults enjoy it. Bronies enjoy it, and go "I see what they did there".
Bad fanservice: Kids and adults go "huh?". Bronies enjoy it and go "I see what they did there".
As far as shout-outs to the brony phenomenon itself, consider this list:http://tvtropes.org/pmwiki/pmwiki.php/ShoutOut/MyLittlePonyFriendshipIsMagic
All of these blend seamlessly into the story, since they're done subtly. If handled correctly, I don't see why more shout-outs to the brony phenomenon couldn't be included.