In what context? It depends on where you're coming from. If it's an e-zine site, there's no reason not to link to both the entire back issue (link to October 06, November 06, etc.) as well as linking to individual articles. In fact, link to the articles from a dozen different places - whatever is convenient for visitors. Take equipment reviews, for instance - link to them from a page listing all past reviews (or pages listing them by category) or from a search page, plus link to them from the individual archived magazines' tables of contents.
In my opinion, PDF is an absolutely terrible format for publishing on the web. It is good for one thing and one thing only: replicating content from a _PRINT_ magazine. It's a good format for a manufacturer that posts on their own website a review from a printed magazine, and wishes to present the article as it appeared in its orginal printed form. To replicate the same review from an e-zine, they just drop the article's text and photos into an HTML page.
For the web and e-zines, all articles should be presented in HTML. There's absolutely no reason to use PDF, but we still see it from publishers with backgrounds in print media that don't understand the power and flexibility afforded them by using all the tools available on the web. Or maybe they have hopes of getting it into print one day when viewership reaches some point (good luck with that), or maybe they just want to pretend that they're publishing a real magazine.
And Word files? You've got to be kidding.
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