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A normal link would read:
<A href='mypage.htm'>Link Text</a>
One using window.location could read
if you want to make sure SEs follow your JS links code them like this (if that's possible):
<a href="mypage.htm" onclick="window.location='mypage.htm';return false;">Link Text</a>
Users with JS disabled and bots follow the first one and users with JS enabled follow the second one.
If it's not possible to code them like that (in a menu) you should use <noscript></noscript> tags with your links in there.