Strictly to be used in UU competition, as it will get eaten alive in most OU games. Ground resistance is nice, and it's one of the few pure Grass-types. Cool Pokémon, but there are better Grass-types for most teams.
Counter is great on Meganium, 100 base in both defenses works excellently. For pseudo-passing and the 50% recovering Synthesis the same cool defenses are a big benefit. Leech Seed is a move every Grass-type should use, can give your team healing support. Too bad Meganium doesn't have better offensive moves. Counter works best with Light Screen, as it will protect you on the Special side while you kill them if they hit you physically.
Razor Leaf is a shafted move in ADV, but a critical hit can mess up things. GrassWhistle is a poor man's Sleep Powder, and again it could hit once. Meganium is very durable and won't mind the accuracy drop as much as fragile Sleepers like Persian would. Toxic is nothing new as an alternative and can work well on something as bulky as Meganium.Substitute + Leech Seed is an interesting combination that should always be mentioned, but Meganium is really too slow to abuse it.
Swords Dance can power up physical moves, but you're probably better off using Victreebel for the STAB on Sludge Bomb. Giving Meganium Hidden Power Fire or Hidden Power Ice will allow you to cover more Pokémon types. Finally, if you are paranoid about being statused, Rest over Synthesis is an option. Don't try Sunny Day or SolarBeam, though; use Vileplume or Exeggutor for that.
If you plan to use Reflect, you'll want to get more Special Defense than suggested above. Alternately, you can use more Special Attack to help a bit with Walrein switches.
Checks and Counters
You'll want to watch out for all Grasses, especially those that carry Toxic or are named Vileplume. Fire-types pretty much prove an end to Meganium. Muk and other Poisons in general will have an easy time switching in and have STAB Sludge Bomb to hit Meganium hard. Tentacruel can turn Leech Seed against you with Liquid Ooze, and set up a Swords Dance sweep, or just straight up Sludge Bomb you.