They are the speed at which data are transferred. ATA100 means it's suppose to transfer data @ 100MB/s (theoritically), but you're in fact transferring at around 50 MB/Sec. Even if you buy an ATA100 or 133 controller card, you might want to know that the PCI bus itself only handles about 100 MB/s and there is lots of other data flowing through it. So 133 means nothing there.
As for the internal/external USB drives, I look at it like this. Anything inside is directly attached to the motherboard for maximum speeds. WIth an external drive, you have a cable you have to plug into. There may be some delay or latency there, but not significant. You'll probably never feel the difference in speed anyways. I would prefer the internal hard drive, but there are cases in which external hard drives are super neat to have. I love to get one for portability.