These workouts (400s fast with short recovery) actually develop your aerobic system. Anytime you are trying to train while "out of breath" and while the byproducts of glcolysis are flooding your system you are trying to increase your ability to sustain that speed without getting "out of breath" or building up those byproducts. The result of this training (400s fast with short recovery) should be that you are able to sustain that same speed without getting quite as fatigued.
When you run these workouts just depends on what race you are running. mid-distance guys would want to do them more often because this type of work is closer to their race demands. Longer distance guys (5k/10) should focus more on work at their race speed. The above type of work (400s fast with short recovery) I think would be better served at the beginning of the training season to "get you in shape". This would also be the time you'd race shorter races in preparation for the longer races later in the season. This is an ideal situation for a college athlete running indoor and outdoor. Focus on the 1500/3k indoor then 5k/10k outdoor. Focus on "getting into shape" with these above workouts and short races along with the usual endurance work. Then when the peak outdoor season comes along you switch focus to your key races and workouts. Mile repeats at 5k pace or 2mile repeats at 10k pace done once once or twice a month as key race prediction workouts. Of course you'd have other workouts to focus on speed and endurance.
Anaerobic workouts (200/400s really fast long recovery) develop sustainable speed. 100-200s I would include all year round because they develop actual top end speed, are a great strength/power workout, and develop neuromuscular control. IE: Short fast reps teach your body how to run effeciently. Really fast 400s with long rest might benefit a mid distance guy, 800-1500m runner as that is close to his race pace.
You know why most coaches want you to run shorter and faster reps at the end of the season? Because they have neglected them the entire year. If you occasionally add in short fast reps throughout the year your body always knows how to run effeciently then and so you can focus your last few weeks of training on what matters most: speed at race effort.
Try this:
Monday: Run an uptempo 5 miles. Record your time.
Wednesday: Run something short and fast, a fartlek, various lengths (1-3 minutes) fast fast fast, but with enough recovery that you're not shit the next day. We are basically working on leg turnover/neuromuscular coordination
Thursday or Friday: Run an uptempo 5 miles Record your time.
My bet is that your 2nd 5 mile tempo will be much faster. Why? Your body learned how to run effeciently the previous day.
3 months of easy summer or winter mileage only teaches you how to run slow. You need to mix it up.
Alan