If it's a sony, the PSU sticking out of the back if just the way they built it for one reason or another.
Ultra=no. Do not get an ultra, they are all bling and no performance. Get a nice Antec, they are killer. Enermax, same as Ultra, no. OCZ are also good, I got my Modstream 520W for $100.
The Molex connector in question, that is just the name of the actual connector itself. The white thing that you plug into the drive or card is the molex connector. When referring to the 12v line, they are talking about the lines that handle that voltage. It is the yellow on. There are three voltage lines on a PSU, 3.3v 5v and 12v, but those are not somethign that you will have to worry about. They are for the modders who need to know where the voltage is on their computer.
Make sure, like the Nube said, have the molex that is going to the card on a single seperate line than everything else.
Those are some very good Antec PSU's on Newegg. In regards to computer stuff, you DO get what you pay for. It is true that, more often than not anyway, if you spend more money you get a better part. You should also check out the OCZ PSU's, they are good. After that, it is entirely up to you whihc one to get. If you are deciding between one from either of thsoe companies, get the one you want. They are both very comprable, and achieve mainly the same result. Meaning, they both rock.
EDIT: took out two of the Antec's because they didnt have Active PFC. Active PFC is Power Factor Correction, and that will stabilize any voltage differences. Always get Active PFC whenevr possible.