If I setup 2 Wordpress blogs hosted on my own server, for example:
Blog #1 - Uses default Twenty Eleven template which comes with WP.
Blog #2 - Uses default Twenty Eleven template which comes with WP but is custom modified with new colours, some small tweaks and a company logo.

Would it make a difference to how either of these blogs ranked? Or would they still be the same?

no. impact at all. Footer links are almost. totally irrelevant.

The reason I thought that it might have mattered is because I thought maybe Google thinks less of those sites using the default template as they appear to be like auto-blogs/little effort made... an exception to the rule almost?

sometimes,blogger shows error,because of the code is directly copied, and Blogger did not interpret it.

Originally Posted by Powelly

The reason I thought that it might have mattered is because I thought maybe Google thinks less of those sites using the default template as they appear to be like auto-blogs/little effort made... an exception to the rule almost?

I would be surprised if that weren't the case. If it didn't make a difference, why would people go out of their way to design fancy new templates?

Actually sometimes it will effect but not all the time and you can take it.

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I feel that unique sites are ranked better.