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For example for Physics, the most relevant other SE sites are probably Maths, StackOverflow and TeX. It would be nice to have the links arranged by relevance, possibly emphasizing the first three or five by a large font size.

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What about when there aren't really any sites of "relevance"? What would Seasoned Advice get? Or Home Improvement? – Grace Note Mar 22 '11 at 12:51
@GraceNote: I'd guess Seasoned Advice could relate to Electronics... But yes, you're right, in case there are no obvious "relevant" other SE sites, the ordering should remain unchanged. (Maybe someone can figure out numbers and a measure how close each site is connected to all others to determine this...) – Tobias Kienzler Mar 22 '11 at 12:55
I'd suggest that Seasoned Advice is more likely than you think to relate to other artistic endeavors. Also what about Homebrew, when it graduates? I think related sites will pop up. – justkt Mar 22 '11 at 12:57
@Tobias the sites that have migration paths are obviously linked together. However, I think it would be better to mimic the same clustering from Area51 on Stack Exchange – Ivo Flipse Mar 22 '11 at 13:22
The footer will need some reorganizing indeed. While valuable for google juice, I distinctly remember Gaming having 5 lines worth of footer links to sister betas at one point... That's some serious footage. – badp Mar 22 '11 at 14:01
@Tobias - How would Seasoned Advice (A cooking site) relate to Electronics Development (An electrical engineering site?) ELECTRONICS IS NOT ABOUT CONSUMER DEVICES!!!! Bah. Though I agree that I'd like to see this feature. – Kevin Vermeer Mar 22 '11 at 17:47
@reemrevnivek: admittedly, it is far fetched unless you try to design your own oven... sorry for the bad example – Tobias Kienzler Mar 23 '11 at 9:04

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