Generally, both bakeries are pretty good, but the question is, what are the differences and which are better? Let's take a look at Samoas versus Caramel deLites.
The Caramel deLites are on the left, and the Samoas are on the right. As you can see, the Caramel deLites have a somewhat lighter color to them, and that's partially because they use milk chocolate as opposed to dark chocolate. Wikipedia says they don't have as much caramel as Samoas, but I'm not sure about that. Personally, I think they're chewier than Samoas, and if I had to choose, I'd choose Samoas. But maybe I'm just weird. I asked around, and there didn't seem to be a consensus. Some people loved one variety, others loved the other, most were indifferent.
So I did a test. I put one box of each on my desk, removed any identification, and put a note up that asked people to try one of each and vote for their preferred cookie. This was a single blind test, and the cookies were labeled only A and B. Ok, so it was hardly a stringent methodology and a lot of people knew which were which just by looking at them, but in the end, it appears that Samoas have a slight edge. A sample size of 8 people is statistically significant enough for me, and it came out 5-3 in favor of Samoas. So there, Samoas are empirically better than Caramel deLites. It's scientific!
A couple of us also compared the Thin Mints (which are the only ones I know of that have the same name no matter what baker), but results were mixed. The cookies are clearly different, and the ABC Bakers (the ones with the prosaic names) Thin Mint actually seems more minty, but they're both pretty good. No stats for this one, but anecdotal evidence suggests that people like the ABC Bakers version better. So there you go. They're both good.
Incidentally, if you can get your hands on Edy's® Girl Scouts® Samoas® Cookie Ice Cream, I highly recommend stocking up. It's available slightly longer than the cookies are, but it'll be gone by March, and it's quite possible the greatest ice cream ever created.