The only major newspaper site successful with a pay-wall (that I'm aware of) is wsj.com. Here's how I think they do it:

1) Give generic information away for free (e.g. Reuters stories).
2) Place any unique, WSJ-only content, behind a pay-wall.

Most content on newspaper websites fall into #1. When you see a link for "all 584 news articles" on Google News for a story, that information is pure commodity. You won't be able to charge for it.

The #2 category is where the money's at, but only if the information is worth something to those buying it. For the WSJ, you have extremely wealthy business people needing detailed info about the economy, and the WSJ is the only place that delivers it. Their pay-wall easily succeeds; high demand for a scarce piece of information, coupled with disposable income to buy it.

How does the WSJ get #2 content? Intimate relationships with corporate executives who don't have all day to talk to dozens of news outlets. Investigative reporting focused on business. Creating unique niche stories which you can't find anywhere else. For example, check out "Off Screen, Porn Sites Trick Advertisers", a pay-wall article:

http://online.wsj.com/article/SB1000142405274870489360457620...

Now search for the story on Google News. 22 hits, none of them relevant, except for the same WSJ article above! The story isn't anywhere else because the WSJ created it. If you're in the online porn business, you're probably signing up for a paid account right about now.

WSJ HACK: If you click on the link in the Google News search results, you'll get free access to the whole article! :) It's the same URL as above, but WSJ.com knows you're coming from Google, and gives you free access. They likely do this for marketing/promotional reasons, and non-tech-savy users won't usually be aware of it.

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The issue with the NYT.com is, while they do create unique content, it's not typically the type of content people want to buy. What's more important to you, a story about a competitor for your business dollars, or an article about which wine tastes best? Are you selling aspirin or vitamins? Aspirin cures pain right now, where vitamins makes you feel a little bit better about your future self.

A few years ago the NYT put their Op-Ed pieces behind a pay-wall, but eventually realized it didn't work:

The paper has tried a pay wall before. In 2005, it rolled out “Times Select” whereby it cordoned off access to op-ed columnists like Thomas Friedman and to archived stories and other features. That strategy generated around $10 million a year. But it was considered a failed experiment, and the Times dropped the wall in September 2007. - http://mediamemo.allthingsd.com/20100120/the-new-york-times-...

Op-Ed is arguably their most unique content, but it wasn't really valuable for their readers. To charge for content, they need unique information that isn't available anywhere else, which is also valuable enough for their customers to pay for. Op-Ed pieces met the first criteria, but not the second.

Perhaps their best way to charge for stuff is to augment it. Shoot a video for every free article, placing it behind a pay-wall. Some people like to watch instead of read. Have a pay-walled "additional details" section, outlining some additional facts not covered in the free article. Subscribers could be the only ones allowed to talk to reporters directly, asking them questions and getting feedback. Stories appear 4 hours earlier for subscribers. I'm brainstorming here (lots of crap, I know).

They're in a tough situation. I think most newspapers have realized that the 40-50% margins from twenty years ago are gone for good. It may be that most of the industry, outside of a niche few, are going to get stuck with much tinier margins indefinitely.