mad0maxx, I assume you mean cat5e/cat6 cables. RJ-45 is a connector type.
If the product complies with the EIA standard for the category, then it should be an interchangable part. That is to say, if I have two different brands' cat5e cables, and both do comply with the standard, and I am using within the limits of the appropriate standard using that cable (e.g., 100BaseTX) then the two should work equally well from an end user perspective. So at that level, yes, they make no difference.
Now, very cheap parts that come out of certain countries have this habit of being labelled fradulently. If the cable claims to be a cat5e cable but really isn't compliant with the standard, then you might have problems.
At this point, I think cat5e is mainstream enough and refined enough that you should be fine. I have seen some no-name cat6 cables on the market that are way too cheap relative to other cat6 products, and I recommend avoiding those. Without high-end diagnostic tools, you won't today be able to determine the difference between cat5e and cat6... so if they stamp "cat6" on the jacket of a cat5e cable and charge a few bucks more, who'd know? I wouldn't put it past shady exporters.
In practice, if you're doing a commercial installation, I'd still recommend sticking with brand-name cable (Belden, Berk-Tek, etc.). I'm not sure if the brand-name cable is that much better, but it's a whole lot safer... and in the grand scheme of a commercial installation you're going to find that buying a little bit better cable is a relatively small expense, while having to redo anything will add up quick. It's just a risk issue.
(actually, if management will pay for it, I always get the best cable I can, but that's just because I really like to have performance headroom. You never know what you'll want to do in the future, and anything that buys more time between redoing the cable plant is usually worth the expense...)