Sometimes I know I end up running my machines too hard and I am not storing them near windows for the hot sun to beat them to death or near a heating vent in my house but other than using a cooling system (I dont want to pay for right now), what are some ways to keep it from getting too warm?

You should make sure your internal fans are still working correctly, that will really affect the performance of you computer. Past that, I don't use a cooling system, but my computer is not in an area that gets very hot (basement office), so I don't need it.