If you plan on publishing the novel, then you need to obtain permission from any and all copyright holders whose trademarks you wish to use in your novel. If you DON'T, then no publisher is going to touch you.

I have read many posts about copyright and trademark law that is just false, so I have decided to clear up some of the confusion. Copyright law does not differentiate between infringements for non-commercial use and for commercial use. Thus, if you copy someone else’s work without their permission (and it is only for personal use) this is still copyright infringement. There are some very narrow exceptions to this rule (such as copying music from a CD to an iPod for personal use), but using a copyrighted graphic in a graphic novel or on a shirt does not fit this exception. However, as a practical matter, it is unlikely that someone is going to come after you for copyright infringement if you are not making a profit. But you should note that many people have been sued for the RIAA for copyright infringement, even though most of the infringers were not making a profit. Trademark law is different. You do not need permission to use a trademark. The key to trademark law is likelihood of confusion. Trademarks are designed to identify a product or service. For example, if your graphic novel featured a band that you called “greenday” this could be a trademark violation. The same is true if you started a band called “greenday”. But if you simply have characters wearing shirts that say “greenday,” this is not a trademark violation. But note, if the shirts use the “greenday” logo, then you may be violating a copyright, but not a trademark. So to sum this up, if the characters in your graphic novel are wearing shirts that say the names of bands in generic font, this is neither a copyright nor a trademark infringement. Copyright requires an actual copy of someone else’s work. Trademark requires using someone else’s trademark in a manner which is likely to confuse the consumer of the origins of the product or service.