There are many different brands of 18650s but the actual cells are made by only a few manufacturers. Sanyo, LG, Samsung and even Sony make good cells but Panasonics are still the most popular and widely available. I believe that the standard 4.2v cells are still only hitting ~3100mah capacity, most of the newest 3400mah cells need a specific charger to hit their full rated 4.35 voltage. Fenix makes great lights and I'm sure they probably both have low voltage warnings or cutoffs but I would still recommend spending a little bit more money on protected batteries in case your charger is not entirely trustworthy or should you buy different flashlights in the future.
In terms of reliable brands there are plenty of options, Fenix of course, FourSevens, Efest, Orbtronic, Keeppower, Eagletac, Redilast, Callie's Kustoms, Xtar, etc. You could also order from someplace like Dealextreme, FastTech, Intl Outdoor, Mtn Electronics and such, like the above mentioned brands they all add protection circuits to the bare cells buy they don't rewrap them and try to sell them as their own brand.
There are some fantastic reviews with lots of test data available here: http://lygte-info.dk/review/batteries2012/Common18650comparator.php
Edit - Just noticed Dallas' reply, AW's are indeed fantastic as well - I actually have 5 of his.