I know it's a big no-no to use a company's name in your domain (like myebay.com), but what about using it prominately on your site. For instance, what if I had a site where I asked the user to choose between ebay or amazon in a form? Could they come after me?
You shouldn't have any problem in using a trademark in a poll. You can always put a disclaimer for the trademark(s) on the page. As long as a reasonable person wouldn't confuse your site with being owned by ebay or amazon, you should be fine. A domain name is an entirely different story - because even if you put a disclaimer on your site, you have already used a trademarked term to get someone to your site. It's like a store - you can sell "Guess jeans" or even have a sign that says "Compare our jeans to Guess" but you can't use "Guess" as the name of your store. A store name and domain name are considered "Servicemarks."
No I wouldn't worry either, as long as you didn't publish anything damanging and untrue about the company you should be fine.