Akali is a char that specialises in killing in 2-3 spells. Her ultimate has an extremely large range so people usualy underestemate it and get inside of it. Her spells have rather small cooldowns so she can take a lot of chars on.
MoA- Mark of the Assassin
TS- Twilight Shroud
CS- Crescent Slash
SD- Shadow dance

I make most of the runes at AP and a few on AD. I take AD so that you still have some power after you use up your spells.

As for masteries I take 21:9:0 with Exaust and Ignite to give my summoner spells some juice. I take some armor and magic resistance to give me the little surviving bonus I need a lot of times.

Start of taking a Long Sword and a Potion. Use MoA to deal some damage to enemy champions. If you can tirgger the mark- then good for you. Try to teamplay a bit at the begining and get a kill or two. when you get 1110 Gold or more go back and take the Giant's belt to give you some HP allowing you to be more offencive. Best usage I see at begining is combinating MoA with TS either use Moa, TS and go hit him or TS, MoA and then hit. you have around half a sec in which when you go out of the TS youre still stealthed. Use that to your advantage. Start going for ganks and get more kills and/or assists. By the time you get Rylai's Crystal Scepter you should be making it as your team's top player. Use your SD to catch up AND slow opponents (remember that you hve Rylai with you now).
Mid-Game
Get The Boots of Swiftness to give you a steady (AND permanent) amount of movement speed.
Start showing the enemy champs who's boss. Be aware of the minimap at all times. concentrate on hunting down enemies. GEt Mejai's Soulstealer to give you an incredible boost of AP on kills and assists.
Late game (End game)
Get Will of Ancients to give you a tramendeous amount of Heal trough your spells. (!~make sure you have at least 5-6 Mejai stacks~!) If youre on low HP creeps like the wrath (jungle creep) can give you the HP you've lost back trough CS. Get the Lich Bane to give you a HUGE amount of damage when you triger MoA and etc. Finaly sell the Long Sword (which I dunno why youre still keeping with you) (probably as a souvenier) and get Rabadon's Deathcap making you a monster deathmachiene. GL and HF. NOW GO KICK SOME BUTT!