Currently, you can't. Sorry =[
But, rest assured, fellow citizen, the New Tab UI is planned to be much, much more customizable "in the future" (which I rekkon' won't be that long, really).
It shall be noted that, in the Dev version of Chrome, you can actually customize it a little bit. You can edit which items you want there, by X-ing them out, and making them disappear, having the next "Most Visited" site take it's place (btw, you can easily go back to original Most Visited layout, so that if you 'X' something out, it's never permanently gone).
You can't re-arrange it or anything like in Safari/Opera, but it's a start, and it's made a difference for me.
If you want to take a gander at the Dev version of Chrome, take a look at the link in my references. When/if you update the Dev version of Chrome, you can easily revert back by simpling uninstalling, then re-installing Chrome. All of your History, Bookmarks and everything else will be kept in-tact, if you do.
*pet* *pet* *pet*
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