I'm struggling to develop a reliable set of moves with middle pairs as well. I think the advice above will be very useful for the games I aspire to be playing in. Less so in the games I'm actually playing in right now. My perception is that the more unsophisticated your oponents are, the more dangerous middle pairs are to play.
I'm playing in low buy-in MTT's (freerolls, micro entries, up to $2 buy-ins) where the play is typically loose and passive. In these games, 2-3 BB raises are not respected. You get called by a wide range of hands including any two face cards, face card-rag suited, any connector, any ace, any pair. A reraise could mean a monster pair or A-J suited or 5-5. Play is usually passive in these games, and it's not uncommon to have 3-5 limpers, so you can see flops cheaply. Unfortunately, that means almost every pot is multi-handed and any flop with an overcard is dangerous.
What I'm doing to survive early in the low buy-in MTTs is this. Throw away low pairs (2-2 thru 5-5, even 6s and 7s on tables with aggressive and/or crazy players behind me) preflop from anywhere, most of the time. Limp with low pairs on rare occasion from LP; no one in these games respects a cut-off or button raise, save your money and don't make them.
With middle pairs (7-7 through J-J in the "kiddie" games), I try to be invisible: see the flop cheaply, keep the pot small. If there are limpers ahead of me, I'll limp along with the crowd, which often works in these games. If the pot is unopened, I'll limp early or raise 2BB middle-late. In multi-way hands, if the set doesn't hit or there are overcards (most flops) I'm done putting money in. I've had very poor luck trying to represent a bigger hand by raising pre-flop in these low buy-in games; I end up getting called down by opponents who will not fold A-3 once their A flops.
If I do hit the set, I try to stay focused and watch for straight and flush draws. I know the prevailing wisdom is to make the chaser pay to hit his flush, but at this level of play, a pot-sized bet doesn't scare off a meathead, at least not early in the tournament. I'll make small value bets as long as the board justifies it. Later, when the quality of play picks up, I might be a little more aggressive with a made set.
I'm looking forward to the day when my bankroll lets me play middle pairs against opponents who outplay me after the flop because they're tough, rather than outdraw me on the flop because they think A-6 offsuit is a good starting hand.