Trackbacks are the messages displayed in the comments list whenever another blog links back to one of your posts. If you use trackbacks on your blog, it is best if they are not mixed with the comments. The comments are a conversation between between real people. Having machine-generated links in the middle of that will only serve to disrupt the conversations.

ProBlogDesign has shared a method that will lift out all of the trackbacks, and then display them as a numbered list after the list of comments is finished. Once you have this done, customizing the trackbacks to appear however you want them to is simple.

P.S. Thank you Eli from Photoshopstar letting me know this lovely WordPress trick.

Source: Separating Trackbacks from Comments