Bayleef is my favourite Pokemon of all time (I know it's a bit unexpected!) so I'll suggest three sets for Meganium :)
Meganium @ Leftovers
Ability: Overgrow
EVs: 128 SpA / 128 Spe / 128 SpD / 128 Def
Timid / Modest Nature
- Leech Seed
- Synthesis
- Giga Drain
- Substitute
Leech Seed is for gradual draining of the foe. Substitute cuts down HP, but it can be recovered through Synthesis. While behind Substitute, drain away the foe's HP by using Giga Drain. This moveset is very limited in terms of coverage, but Meganium can be switched out after setting up Leech Seed though it may be not recommended. However, Meganium can prove to be a good staller even against Pokemon with type advantages if used wisely.
Meganium @ Leftovers
Ability: Overgrow
EVs: 252 SpA / 252 Spe / 4 HP
Modest / Timid Nature
- Sweet Scent
- Leech Seed
- Petal Dance / Energy Ball / Magical Leaf
- Hidden Power [Rock]
You've probably notice that no matter how you go, you can't run away from upping Meganium's defenses. Sweet Scent + Leech Seed combo gives you a higher chance of dodging your opponent's attacks and gaining more HP. The main idea is to up its lackluster speed so it will get to move first. I prefer Timid nature for it. Petal Dance / Energy Ball / Magical Leaf is STAB and you choose what you prefer. Personally, I will go for either Petal Dance (greater power) or Magical Leaf (never miss). Energy Ball is kind of... in between. But it's up to you. Hidden Power [Rock] is for coverage against Meganium's many weaknesses but namely Flying, Fire, Bug and Ice.
Meganium @ Light Clay
Ability: Overgrow / Leaf Guard
EVs: 252 HP / 128 Def / 128 SpD
Bold / Calm Nature
- Aromatherapy / Heal Pulse
- Light Screen
- Reflect
- Synthesis
This moveset is quite strange, but as its role suggests, Meganium will be delegated to a Support position. Aromatherapy heals the status problems of all Pokemon in your party which may be useful, and with Light Clay, the effects of Light Screen and Reflect last for 8 turns. You use 2 turns to set up, 1 turn to switch in, and your next Pokemon will have 5 turns of great Special and Physical Defenses. Meanwhile, Synthesis is for setting up and healing Meganium. However, if you wish to Heal Pulse may be better as you can try to heal more Pokemon while using Synthesis as well before using Light Screen and Reflect, then switching out. I have a feeling that few people will want to risk this, but just throwing all the options out.
There you have it! Hopefully this helps :P