Level-Up moves (18-1=17):
0 - Bite - Snakes bite.
0 - Leer - Physical Pokémon, and most snakes get it.
0 - Vine Whip - Whip that tail!
0 - Wrap - Snakes wrap around you and squeeze you and kill you.
6 - &Leer - See above.
10 - Sweet Scent - Man, apples smell great!
14 - Glare* - Dem eyes. They be starin'. Best form of paralysis, very useful.
18 - Scary Face - His face looks scary. VERY useful for him, as it can freeze a switch-in and allow Malaconda to get a hit, whether with U-Turn to switch out or with Power Whip or a Dark STAB.
23 - Razor Leaf - He can shoot his eyebrows at his opponents. Basic STAB for low levels.
27 - Twineedle - Pretty weak move, but gives him a Bug attack for hitting Grass and Dark Pokémon, and he can use it by shooting out needles. Cloyster gets it, so I don't see why Malaconda wouldn't.
31 - Crunch* - Bite evolved into Crunch! Basic Dark STAB for all levels.
35 - Flatter - He's a charming devil (all puns intended).
38 - Poison Fang - He is a snake. He has fangs. Poisonous fangs. His only real way to hit Grassmons hard.
42 - Nasty Plot*! - He's evil, of course he's plotting! Pretty useless on him though.
45 - Spikes* - Why wouldn't he be able to shoot all those spikes on his body around his enemy and leave them there? Left out Rapid Spin in exchange for Spikes because no Grass or Dark Pokémon has ever had Rapid Spin while both have had Spikes.
50 - Power Whip* - The best Grass STAB in the game, and his most useful STAB. Hits hard off that high Attack stat.
56 - Aromatherapy* -
Mmmmmm, I like apples. I feel better now.
62 - Tail Glow* - The golden apple shines, preparing him to use, what, 6 different Special attacks? No Baton Pass so that people will have to watch out for special sweepers. Easy to use on the switch.
TM/HM moves (26):
TM06 Toxic* - Every Snake has poison! Learned by almost everything.
TM10 Hidden Power* - Anything that can learn TMs...
TM11 Sunny Day - Grass-type, Harvest... Just in general, he's made to be a Sunnymon.
TM12 Taunt* - He's not giving you that apple, bitch! He's just taunting you. Useful on the switch in if they switch in Ferrothorn, etc. which walls Malaconda.
TM17 Protect* - Anything that can learn TMs...
TM21 Frustration* - He's MAD. VERY mad. Good Normal attack.
TM22 SolarBeam - He's grassy, and he needs SOME special attacks.
TM27 Return*^ - He's HAPPY. VERY happy. Good Normal attack.
TM32 Double Team - Snake army, unite! Almost everything learns it.
TM41 Torment - He's not just taunting you, he's
tormenting you. Flavor Dark move.
TM44 Rest* - Snakes like to take naps in the sun. True story. No but seriously, Rest is everywhere.
TM45 Attract - He can charm the ladies with his apple. Useless, basically.
TM46 Thief - He is greedy, he will steal your stuff cuz he's Dark. Dark move, could be fun on an Infiltrator moveset.
TM48 Round - Anything that can learn TMs...
TM53 Energy Ball* - Grass special STAB. Most Grass-types get it.
TM56 Fling - He can swing his tail. It makes sense that he could fling an item with his tail. Seems like it could make a fun gimmicky move, kinda like Iron Ball Tyranitar.
TM66 Payback* - Strong Dark STAB, a bit harder hitting than Crunch, works well with his slow speed.
TM67 Retaliate - He gets really angry when you kill his teammates. Furthermore, he's a pivot, so it makes sense for him to be able to be a revenge switch-in, too, although not a revenge killer due to his speed.
TM70 Flash - Dat apple can shine!
TM77 Psych Up - He always stays one step ahead of his opponents. If they boost, so does he. This gives him an unreliable way to boost even stats which he can't normally boost.
TM82 Dragon Tail* - Lickitung gets it. Lickitung. The important thing is that Serperior gets it, and that gives precedent for the next Grass snake to get it. He swings the tail hard enough to be a Power Whip, so it must be hard enough to knock the opponents back.
TM87 Swagger - Almost everything gets it, and he has Flatter, too, so this makes sense.
TM89 U-Turn* - Because snakes are always found in the shape of a U. Also, he is a pivot, so it makes sense.
TM90 Substitute* - Most things get this. It makes sense, as he is evil, that he would substitute himself, protecting himself at all costs.
TM95 Snarl - A rare move, but it makes sense, especially since it is Dark.
HM04 Strength - Serperior, Seviper, and Arbok all learn it. I figure snakes must have a lot more strength than they seem to. High Attack stat supports it.
Move Tutor moves (11):
Dark Pulse* - Special Dark STAB, most Dark-types get it, and it's a pretty useful move. The apple dims to black, then shoots out the pulse of darkness.
Foul Play* - Snakes never play fair, especially ones which try to trick you with apples. Good physical STAB to abuse against his physical counter switch-ins.
Gastro Acid - Snakes have lots of acid inside them. They spit it up to remove their opponents' abilities.
Giga Drain* - Good special Grass STAB, allows a special build to be viable and free up the moveslot that would otherwise carry Synthesis.
Iron Tail* - His tail is literally the most powerful thing in the world, I swear. Iron hits a lot neutrally which his STAB attacks wouldn't (Hydreigon, for example).
Knock Off* - Because fuck items, man. I hate them. They should all just go away. Useful for the free hit on switch-ins as well as to weaken or cripple them.
Seed Bomb* - Weaker physical STAB which doesn't miss, unlike Power Whip.
Sleep Talk* - Because how else is he going to kill things while he sleeps?
Snore - Oh, that's how.
Super Fang* - His fangs are pretty prominent, and with this, he would be able to weaken any switch-in drastically off the bat, then pivot out to something which can finish it.
Synthesis* - It makes sense, since he loves the sun so much. Best recovery move for him, not useful on rain but amazing in sun.
Egg moves (Field and Dragon Egg Groups) (11-2=9):
Body Slam - A less viable form of paralysis caused by slamming his body into his opponent. Glare is better, but Body Slam has its uses as a Normal attack to hit a lot neutrally.
Captivate - Because he wasn't a good enough special wall already. That apple draws all the attention from him :'(
Lick - Other snakes can teach him to lick his opponent, which is really not useful in the slightest.
Mean Look* - Well, seeing as he has a scary face and can leer at the opponent, a mean look isn't that big of a deal. It's not that good of a move, but it could be useful at times to trap a troublesome opponent.
&Poison Fang - See above.
Poison Tail - Because his tail has spikes in it with which to stab into the enemy and inject his venom. It is also an alright attack for an egg.
Punishment - He's the mighty snake! He can punish whoever he sees fit. However, he usually punishes the opponents who try to boost their stats without caring about him.
Pursuit* - Snakes can move surprisingly fast. He can chase his opponent, then murder them. A pursuit trapper suits him, especially since he is slow.
&Scary Face - See above.
Thunder Fang* - Only electric attack he can learn, it gives him a good attack with which to hit Steel-types neutrally, which he otherwise would not be able to hit.
Wring Out - Snakes will wrap around you then squeeze you until you die. Even if you are a Wailord. Regardless, it is a flavor move.