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Sandip it sounds like you are providing advice for an affiliate. JB85 is asking about affiliate links because he is a merchant. JB85 are you going to go through an affiliate network like Commission Junction, Shareasale, Linkshare, Google Affiliate Network.... or are you going to have the links go directly to your site via some internal affiliate management system or script? If you go through a major network you don't have to worry about it. The links go through the network's URL first and do not pass pagerank. If you have the links go directly to your site you should not try to get pagerank through them. Add a rel nofollow tag to the text you provide affilaites, and state that the links must be nofollowed in your terms. It may seem like a good idea to use "naked links" but it would be short-term gain and long-term loss for any eCommerce business hoping to generate organic search revenue in the coming years. Good luck!

I don't think it matters much which order if you're talking about the SEO benefit of where the keyword is. To me, it just makes more logical sense to choose www.companynamejobs.com from an English language standpoint. If my choice was between "SEOmozjobs.com" and "jobsSEOmoz.com" I would choose the first one (although they both look a little like spam to me, which is why I still think using a subfolder is better)