It's All About Timing.
Time is our most precious resource. Once it's gone, we can't get it back. This is why in the gym, you want to get the maximum amount of gain for the least amount of time. While most people track their reps and number of sets, few people are tracking the order in which they do their exercises...and that's a problem.
The order in which you do your exercises effect the muscles you fatigue, and that in turn effects how much you can lift. The general rule is to do the heavy lifting (big muscle exercises) first, then smaller muscles after.
If you're doing a weights/cardio split or have cardio anywhere near a day of lifting, you want to put the lifting first. Extensive cardio can fatigue muscle, wear away at muscle gains, and sap strength. You don't want that a day before a day of compound movements. Set yourself up for success and do heavy movements first as it will add muscle that can actually help you in your cardio. Anyone who has ran a day after lifting knows the extra muscle mass gives you a pep in your step, unfortunately it doesn't work the other way around.
In regards to which body parts to hit first. You want to concentrate on the big muscle group exercises first and then the smaller groups after. For example, if your set consists of deadlifts, shoulder presses, and triceps extensions, you want to do the deadlifts and shoulder press first, and then the triceps. The reasoning behind this is that isolation exercises tire out the smaller muscles which take away from compound mass building exercises. When you can't perform these exercises to their full potential, you take away from your over gains and muscle mass. Get it?
Another golden rule is to put free weights before exercise machines. As well all know, free weight exercises tend to put more of a strain on the body because not only do you have to move the weight in one motion but because there's nothing supporting the weight your body also has to balance and coordinate. Great way to get shredded. This makes dumbbell/barbell exercises slightly harder, meaning you require the most energy and strength to perform these exercises at your max lift. Free weights first, then machines, that's the rule.
To be honest, these supposedly hard and fast rules are highly pliable. Depending on your genetics and the training you're use to, it's not a crime to mix and match. Try it our way and then personalize your lineup to craft your perfect physique.