msi ge60 2pc apache or asus n550 jk?

They're going to be pretty much identical since the specs are. You'll see very slightly better performance with the 7200rpm drive and slightly worse battery life (probably insignificant considering the rest of the specs). In my experience, MSI has had some quality control issues in the past with their motherboards, but every manufacturer has their defects now and then, so it's a tough thing to try and predict.

I will say Asus tends to stop supporting their laptop drivers sooner. I've got an N53SV which was a nightmare trying to find working Windows 8 drivers for, despite being purchased only a year before W8 came out. If that's a concern for you (you want to upgrade to windows 9 when it comes out), you may want to check out how long MSI supports their laptops and provides updated drivers.

Honestly I would upgrade both to a SSD for faster HD performance. I'm not sure about mSATA as I've never used it, but if you want to do a small SSD for OS and a data drive for the rest, it might not be a bad idea (it's what I do on my desktop). Just keep in mind that'll drop your battery life even more.

GDDR5 would have better performance, but only very slightly. Technically it's based off of DDR3, but has a few optimizations and better bandwidth than regular DDR3.

I don't know if anyone can clear, I've had troubles with the solution thing myself. But yes, Asus better in terms of battery (slightly) and they have a slightly better reliability rating, but the MSI is higher in terms of raw performance and upgrade options (msata)

You're welcome. Honestly I have no idea, but they're both going to be gigabit ports. It's probably just a fancy name for an ethernet driver that's the same as all the others. It might have software that will prioritize certain applications over others, but a more pressing concern would be your own internet's line quality and speed first, as the ethernet port is almost never a bottleneck.