If you need the portability...externals are OK.
I don't like the fact that data transfers are appreciably slower than with drives directly connected to the motherboard or a PCI controller card...but that's just my idiosyncratic beef
Logically, it makes troubleshooting issues with a drive more complex...because you add in the possibilities of problems with the enclosure to the possibility of problems with the drive...and it creates what I consider an unnecessary factor in problematical circumstances.
Added to that...bare drives are significantly cheaper (1TB drives at $69 last week, I think).
And...by all means, get SATA drives...even if you have to add a controller card.
Drive preference...is just that, drive preference. I've had Maxtor, IBM, Hitachi, WD, Seagate, etc...I have more Samsung drives than any other brand (because the price was right) and I can't say that any brand is "better" than another.
If you are concerned about drive failures...get drives with at least a 3-year warranty. If you get 3 years out of a drive you paid less than $100 for...I'd say that you got more than your money's worth. I still have drives which were made in 2001/2002 and they still perform...but they are IDE and have been made obsolete by the much faster SATA drives with larger capacities now available.