If your app is just showing somewhere lists of brands and doesn't misrepresent anything - then it's absolutely OK (that's what brands are for). You can make an app, that searches through amazon or ebay (for example). So you can have buttons "Amazon" and "Ebay". But if your "Ebay" button will load your web-site, where you sell something - it's illegal.
If you want to make things completely clear - you have to mention somewhere "Ebay is trademark of blablabla" "Yellow pages is trademark of blablabla".
If you are gonna use "ebay" as part of your app name.. well.. then it's a gray area. Ebay may not like it, if they don't - they will send you/Apple notice and you will have to change it.
This is from legal point. In general it seems Apple doesn't want to get involved in legal battles and since Apple is hosting and distributing the applications it is responsible for the content of all the apps. Therefore Apple is trying to avoid the trouble by usually following "cease and desist" notices. So.. even if you are perfectly legal Apple still might take your app down if somebody sends legal notice to Apple. You will need to convince Apple that you are not doing anything illegal and maybe negotiate with the owner of trademark. Or upon receiving such notice - just remove the offending name and continue. It's a no big deal actually.
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