Internal drives are supposed to be faster, but it's not recommended to work on them because you could lose everything if your computer breaks or is stolen. But what produces the fastest render times?
For example is it best to have your media and project on an external firewire drive and render to the internal? Or vice versa? Specifically with a Mac Pro and After Effects.

eSATA drives are as fast as internal drives, sometimes even faster. Firewire 800 is a close second. Forget USB and firewire 400.

BTW, external drives can break just as easily as your computer. They can also be stolen too.

external hard drives - eSATA connection. I would stay away from firewire and USB since the standards can change soon and eSATA is the best bet. However, firewire is the next best option for rendering and using after effects. The most important thing is to always have a large amount of RAM as well.

USB 3 is out now. Will likely take a bit till it's in all the new hardware but it has speeds up to 4.8 Gbps. Wish my fairly new MB had it.

There's an external Black Magic Intensity box that uses USB 3. HArdrive cases can't be far off.

I think it will pass by eSATA only because you can still plugs usb 1 and 2 devices into a usb3 port. Can't do that with eSATA.

USB 3 Connectors are the same as 1 and 2. USB 3 Cables are not.

There are also hot swappable SATA bays for hard drives.

I like externals for portability. You can move from station to station if needed. You can also grab them in a hurry if your house catches on fire!
Big deal with externals quality case. A cheap enclosure with crappy electronics can be a nightmare.

you can still plugs usb 1 and 2 devices into a usb3 port. Can't do that with eSATA.

Actually, you can. My laptop has an eSATA/USB combo port. It takes USB 1.1, USB 2.0 and eSATA. Pretty clever.

Neat.

Well if I upgrade my Brand new MB with USB3 I'll have to make sure it's a ESATA/USB3 combo.

Can't believe my new MB is lacking both!

I just installed a 2TB HD. I like that you can't accidentally unplug it.

Next I'll probably put a 2TB in an enclosure for portability.

I run raid configured HDs externally and have backup running to protect them. Its not going to make an enourmous difference for you in AE or another compositing program though since each frame renders so slowly in most cases. Its more important in this case to get as much RAM as you can.

I have to format my new external firewire drive for my mac. I used to select "journaled" but someone said for video it's best to be non-journaled. Which is better?

There is no difference in formatting of a basic (non RAIDed) disc whether it is in a USB enclosure, an eSATA enclosure or on a SATA connection but stored inside your machine....so there is no difference in risk.

I think the risk people talk of is when discs are under a RAID arrangement off the motherboard or other raid controller AND THE RAID CONFIGURATION IS NOT BACKED UP. [sad voice of experience here]

I have had a nonRAIDED root discs where the boot sector went bad or OS was unbootable, moved it to a different machine and recovered all the user data off of it.

Use computers long enough and you will get much "training" you did not bargain for!

Well... it does have to be in a format that the computers you will be using it with will read. You have to install software to read a mac filesystem in windows, for example.