YUCK!
I'm sorry, but I really dislike drop-down menus. Actually, I hate everything that requires javascript!
Javascript is so riddled with security holes and gives such a poor tradeoff between added utility and annoyance (e.g. drop-down menus vs. having to deal with pop-ups) that I simply leave it turned off. If you want me to stop looking at ENWorld past the front page and bulletin boards, by all means, go ahead and use the drop-down menus.
At the very least you would need to provide an alternative way to navigate your site. That means implementing (and updating) all the navigation TWICE, so more work for you.
That being said... I *did* turn on javascript to check out the drop-down menus, and I have to say they look rather bad on my machine (Linux box using Netscape). In both versions "D20 System" is split over two lines, making it fail to line up with the other menus. In the menu-on-top version, the highlighting when you move over the top menu items is offset from the menu item, overlapping it to the left and slightly up. In both version, the highlighting for sub-menus (especially with multi-line entries) is also off significantly. There errors seem to happen even on brothercake's own website.
For example: when I select "Hosted" on the menu-on-top page, a highlighted "Hosted" is displayed, overlapping almost half of the "Archive" menu item to the left of it. Then when I go down to "Crooked Staff Productions", the highlighting overlaps with the second line of the previous item (where it says "Design" in "Claudio Pozas Art & Design"). When I move to "Natural 20 Press", the submenu for "Asgard" comes up to the right of "Crooked Staff Productions", and I have to move my cursor quickly up and right to be able to "catch" that submenu before it disappears. Moving even further down, when my cursor is over "Malls & Morons", a highlighted "Malls & Morons" is displayed, partially overlapping the entry for "Dusk" several entries up! (I'll post some screenshots if people are interested.)
I have seen dropdown menu systems that worked fine under my configuration, but this is *definitely* not one of them!
OK, enough bitching...

time for some constructive suggestions. I think the best single thing you could do for the front page is to do away with the three column format. I was really struck by how much legible everything became on the menu-on-top page, simply because you got rid of that left hand column. Ignore the menus for a second, and compare the original page (wide left column) with the menu-on-left page (narrower left column with the menus) and the menu-on-top page (no left column). In the first one, I typically have to scroll down 2-3 pages just to read one day's news. The latter shows me almost an entire days' news on the very first page.
I would suggest (again) you do away with the entire rightmost column. Then we can restructure the current menus on the left a bit and presto: huge improvement in usability and looks.