What could it be that after driving for 30 mins or so and my car has heated up, it begins to make a really loud humming noise seemingly from the rear of the car? When i apply the brakes it stops.

Rub your hand over the tread and try and feel for cupping or uneven tread patterns. This will create alot of road noise. If not, have your wheel bearings checked.

Check air filter and catalytic converter and muffler for good flow

That could be anything - from tire noise to bearing noise to the passenger in the rear seat! Where does the noise seem to be coming from - front? rear? left? right? engine? Is there anytime that the noise changes or goes away? Gets louder or softer? All these things help us to help you. Year and engine size are helpful too.

it could be center bearing, if its going bad it can also cause a vibration, make sure you have sufficient fluid in the diff as well, you can also get a noise and vibration from collapsed motor or trans mounts

If the noise get louder as you speed up, it is possibly a wheel bearing, needs checking out by a mechanic.

There is bulletin for a humming noise like yours that has to do with the Torque Converter. #01-07-30-010C 5/12/2008 Call GM and ask about it.

When does the noise occur, while driving only, or driving and idle, in gear, or in neutral and park? If it occurs all the time (while driving and at a stand still in cold weather) it could be the fuel pump. If it occurs only while driving, it may be a wheel bearing. Describe the noise (humming, grinding, whirring, etc), and what is the mileage on the Pilot? Answer my questions so I can fine tune my answer. Thanks!

Chances are it's the tires rather than the engine.
Does the hum diminish if you back off the accelerator? If yes, then look at rear axle pinion bearing. If no, then feel across the tires. They should be smooth across. If they're rough, they will make a loud howling noise.

clunking or grinding noises, wont accelerate to full potential,

It's the wheel bearing. Guaranteed. Just replaced mine. Go to Audiworld tech articles for step by step instructions on how to test the wheel bearings. They must have been put in wrong last time or they just went out again.