Halo CE: Shotgun, Shotgun, and more Shotgun. Also I like the Rocket Launcher for when there are large groups.
Halo 2: Energy Sword. If an Energy Sword is not present, Shotgun. I like the Major Sentinel Beam or a Rocket Launcher as a backup.
Halo 3: There are a lot of good weapons to use against them, and it varies with each level the Flood appear in.
In Floodgate, I use the Gravity Hammer (switching to a Shotgun or Brute Shot later on) with either a Carbine or a Battle Rifle as my secondary weapon. Either one gets rid of those pesky Ranged Pure Forms.
In the Covenant, I use plasma weaponry, starting with a Plasma Turret and then Plasma Rifles. They tear Flood up! When the Flood appear in that level, I typically have a Fuel Rod Gun in case I get angry and turn green.
In Cortana, I use an Energy Sword/Gravity Hammer and a Brute Shot. The Brute Shot is more than capable of hitting enemies within each room, and can kill most Combat Forms in one hit. If it doesn't and they get too close, mash them up with the blade! The only problem is that ammo is relatively scarce, so I frequently switch to a Carbine.
And finally in Halo, I use a Battle Rifle and a Fuel Rod Gun. The Battle Rifle allows you to pick off Combat Forms from a distance. Aim for the chest and they'll go down in one hit. Eventually I abandon the Battle Rifle for a Brute Shot, as ammo is quite plentiful and that blade is a good substitute for an Energy Sword. Then I swap out for garbage weapons to fight Spark, as you lose whatever weapons you enter the fight with. Pick up your weapons afterwards, and finish the fight!