window.location.href returns the location of the current page.
top.location.href (which is an alias of window.top.location.href) returns the location of the topmost window in the window hierarchy. If a window has no parent, top is a reference to itself (in other words, window === window.top).
top is useful both when you're dealing with frames and when dealing with windows which have been opened by other pages. For example, if you have a page called test.html with the following script:
var newWin=window.open('about:blank','test','width=100,height=100');
newWin.document.write('<script>alert(top.location.href);</script>');
The resulting alert will have the full path to test.html – not about:blank, which is what window.location.href would return.
To answer your question about redirecting, go with window.location.assign(url);