Here are some helpful tips on dealing with enemies as you progress though the game.
Respawning[edit]
Dinosaur enemies never respawn (come back after you eliminate them). The two weakest gunman types will always respawn when you're about a screenful away from where they were. Stronger enemies like the grenadier and the flamethrower never respawn. Note that enemies of all types do respawn if you leave an area through a door and come back to it later.
Fighting Velociraptors[edit]
Fighting velociraptors is usually easy, though it can be tricky in close quarters. The easiest way is to equip the shotgun and give them a few blasts. Sometimes you'll be using the cattle prod for most of the mission, or you want to conserve shotgun ammo, so you'd like to take the raptors out with the prod instead. For this you'll want to have a little space; if it's cramped you may want the tranq bazooka instead, though you may suffer some minor splash damage. Anyway, the raptors follow a very basic pattern. Just stand still while you charge your cattle prod and wait for them to jump at you, and time your jump so that you pass over them. Then turn around and fire at them. You can also repeatedly tap 
for a couple more weak shots afterward to quickly defeat brown (medium-strength) raptors on the easy and normal difficulty settings, but grey raptors will need another full-power shot.
Fighting Flamethrowers[edit]
Many of the levels have flamethrowers positioned in a way that you'll probably get fried if you try to confront them with the rifle or machine gun. For example, a flamethrower might be positioned just behind a large crate that stops your bullets, but not his flames. Usually you can defeat them by standing at a distance, jumping, and firing the shotgun. Probably only one of the three pellets will hit, so it will take a few shots, but it's better than getting toasted.
Alternately, you can duck behind the barrier (if it's the sort that rifle and machine gun bullets are just barely unable to clear while you stand still) and wait for his flames to stop (he should be at such a range that he will not change to low-angle firing and his flames will stay over your head). Stand up and fire the shotgun, ducking again if you are unable to dispatch him before he starts shooting again. Repeat until he is dead.