That is becoming the age old question these days when purchasing any computers or hardware. Basically the answer to the question is simple, which ever one you choose will be perfectly fine. And this post of mine might spark a nerve with people but it is very true. If you prefer intel go with intel if you perfer amd go with them.
There are subtle differences with both of the companies, and as you would expect each of the companies have a full line up of products from the entry level processors to the server tower processors. I don't know of any reason why you wouldn't choose a brand over the other. They both perform relatively the same, and in my house we have 2 amd laptops and 1 intel laptop which are comparable in specs and haven't (won't) see a difference between the processors.
AMD are great processors and any one that has been watching that space has definitly seen amd come out of the shadows and put intel on their heels to keep up with them. There have been speculations that AMD produce less heat but that is still not quantified properly.
Now what you do need to understand is the different levels of processors that each company offers and which best supports what you are trying to achieve. Now that is a completely different topic all together.
Overall I wouldn't put any extra stock in one over the other.