I am building a new rig and I have a rather new 3TB Seagate external HD. Was wondering if I am able to use this as an internal HD and if there will be any complications or implications on performance? (As compared to a WD Black 1TB 7200rpm)
No you cannot use it internal. According to my knowledge it is better if you find an internal hard disk. It has a better performance than the USB 3.0 port because the sata is 6.0 Gb/s (768mbs) and USB 3.0 is 30MB/s read and 24MB/s write.
@ltng, if you intend to remove the 3TB HDD from its enclosure and install it inside your PC, then, depending on your hardware, it should be possible to do so. Just be aware that Seagate often uses slower Green drives in its external products.
To backup what fzabkar (not that fzabkar needs any backup from me) stated about Seagate external drives I will mention that I have a LaCie external drive enclosure which actually contains a Seagate 2TB drive and according to the specs it spins at 5900 rpm. I have seen it listed as a Green drive.