The advantage of using pdf is that the design is "locked in" when it is created. The user has little control and cannot change font, text or format. For designers this is a bonus as their baby can't be mangled by such things as browser version or screen size. However, there is no elastic of liquid layout which can prove a problem given that different devices have different aspect ratios. Users end up moving the document around or zooming in and out to see the whole page.
Interactive pdfs can include buttons, hyperlinks, page transitions, embedded swf and videos (see my link at the bottom on making interactive pdfs)
The epub format is used by Kindle, Nook and other e-books. It is styled like a simple version of XHTML with CSS, and includes interactive table of contents (hyperlinks) and images placed as anchored objects. The disadvantage for designers is that style (size, layout, font, etc) and layout control is based on the capabilities of the end device. This is designed for text (books) rather than magazines that require quality photography (colour!) and typography.
The .issue format is a content file that requires a digital content viewer (device specific) to "play" the digital magazine. The .issue file bundles separate horizontal and vertical layouts (think of a tablet as it's flipped from portrait to landscape). It can include page transitions, animation, video, interactivity and is touch interface friendly. However, it is all too easy to create digital magazines with huge file sizes!! Many apps for digital magazines (Wired mag) are in fact just branded digital content viewers that downloads the latest .issue file.
Keep tuned to this blog - time permitting I'll write more detail about both the .epub and .issue formats and how to actually make digital magazines. COMMENT on this post about digital magazine formats that you would like to see covered in more depth.
For information on interactive pdfs take a look at the Web Devil tips on how to make interactive pdfs using Adobe InDesign.