The website is looking really, really slick right now. It's taken a number of steps forward since you first started; nice work. I have a few of points of constructive feedback and then a bunch of ideas to run past you to see if they stick.
On the article page, I notice that you have the email at the bottom of the post. Ideally, you shouldn't be embedding those in the body content, but rather exposing the author's email address (if you want people to access it) with WordPress. There's a function you can use to get the author's email address and show it in the template. Additionally, instead of placing this at the bottom of the article, I'd focus on having an author bio section near the top that includes the name, their Twitter account, a link to the most recent posts, etc.
Two more things for the article page. I think the font color you're using, although it fits nicely with the color scheme you have, isn't very readable. I'd make it darker and potentially a bit larger. Additionally, you shouldn't have the location in the body content either. If you want to keep the location associated with the article, then there's a cool plugin called GeoPress for that. What you do is store all of the locations as custom fields associated with the post, and then it will allow you to generate maps of all your posts, etc. By keeping the metadata as metadata, you can use the aggregate of it as something useful. It's also a simple thing to expose the data if you want it to look the exact same to the end user (although you could also place the article on an inline map, etc.)
Like Joey said, I think you're 80% of the way there with your logo. If I were working on it, I'd drop the tagline from the logo, add it to the title tag for SEO, and come up with something (possibly a secondary logo), that will work for square avatars too.
The home page is coming along nice. I have a couple of ideas to throw at you. One, what do you think about adding the author name and tags to each of the story elements? Two, I think the "What We're Reading" widget could use a bit of padding and rearranging. I might move the author name to the front of the comment, and you could easily add a link to a What We're Reading page (a la this and this).
Ok, time for the more forward thinking ideas. On the Spokesman-Review website, they have navigation at the top called "Quick Links":
The whole idea is to give you ready access to the story you're most likely coming to the website for (i.e. the big stories that day or week). I think it would play well with a student newspaper too, and look and work nicely under the main navigation bar on your website. On the top, you've got the more traditional methods of categorizing news content, but underneath the links are the "trending" topics. Does that make sense? The links would drive either to stories in progress or topical landing pages, and it might even be worthwhile to build a little plugin that arranges and prioritizes the links so that the editor doesn't have to change the WordPress template.
I think you should approach the category pages as landing pages on their own right. Currently, they're formatted more in the blog/chronological format. It would be really cool if each category page had the option to highlight big images at the top, a video, etc. Basically, the nice way that your home page looks should also apply to your category pages.
The final thought is to have a page (which people can choose as their default page when they sign in) which aggregates the stream of all of the activity on the site and in the community. This would include new posts, new comments, tweets from the geographic area, photos recently uploaded to Flickr, etc. and might take a similar design approach to Facebook or the new AnnArbor.com.
Good luck! Looking forward to the continued progress