Scanners - You'll see a few of these annoying guys near the beginning. They're aren't much of a threat right now.
Civil Protection - There are a few of these weak soldiers hanging around at the start of the battle. You'll come across them occasionally mixed in with the normal soldiers.
Hoppers - These mines are smart enough to leap up and launch themselves at any nearby enemies. They make one clicking sound when you are dangerously close. They click twice to launch into the air and attack. If they are in the air, switch to the gravity gun and catch them to stop the blast. If you see them in time, then use the gravity gun to rip them out of the ground and switch them over to a friendly AI.
Combine - Average soldiers that are standing between you and the Citadel. Aim for the head.
Combine Elites - These white suited soldiers are well armed and very dangerous. They can use the secondary fire of the AR2 to take off about 1/3 of your health. Use heavy weapons like the crossbow, grenades, or the secondary function on the AR2 to take them out.
Man Hacks - These annoying guys are all over the place. Be ready to fight them off. Just use the gravity gun to grab them and throw them into the wall.
Striders - You won't have to fight one of these guys just yet. They are around though. If you rush into their line of sight, then they might send a few shots your way.
Headcrabs - These guys are spread throughout some of City 17. Keep an eye out for them.
Zombies - Your old friends are hanging out in the toxic pool and the sewer. Blast them.
Fast Headcrabs - A few of these guys come out of the rockets. Blast them.
Fast Zombies - You'll see a few of them around the Combine bases and the Sewer. Take them out quickly with the old shotgun.
Poison Headcrabs - These guys are in the sewer for a few bits. Keep an eye out for them.
Barnacles - These guys are still around too. Just don't step into them. They will actually eat a lot of enemies too, so don't be too quick to kill them.