Karen and I have been using our iPod touch devices for several years. We love them (me perhaps slightly more), and use them for checking email, looking up recipes, looking at maps, and playing music through Pandora while we're at home. They're also pretty resilient, our older one still works properly despite me putting a long crack down the center of the screen while camping in Death Valley last summer.
A few months ago I found a really nice iPod application called Discover. It should also work for the iPhone and iPad. I am using the free version which is ad-supported.
Basically, when you run the app it will connect through any wireless network you have previously set up in the iPod Settings menu. When the app starts up, it creates a server on the iPod which you can upload files to and download files from. It makes a really cool file-transfer devices, but an even cooler scientific PDF reader. At first I was worried that it would be annoying to upload files through my web browser, but you can select many files at once (even whole directories), and they're all uploaded at the same time. The upload speed is also much faster than if it were going through the internet because the transfer happens on your local wireless network. For me it takes less than a minute to transfer 30 papers to the iPod.
Once you have uploaded the papers to the iPod, you browse to the papers from inside the Discover App, and read them by double clicking on the file. The PDF reader uses the same multi-touch as other iPod applications, using pinching to zoom, and pulling to scroll. Because the screen is a full color display with a fast refresh rate, it is like looking through a small window onto a printed journal page. However, because of the zoom feature, it is actually more convenient for looking at color figures than reading a PDF on a computer screen. I think that the iPod is better for color figures than the Kindle, though there are relatively few journal articles with color figures. It also handles the transition between individual pages really well, since it simply concatenates the beginning of each new page to the end of each old page, so there is no big whitespace gap between pages. It also automatically rotates the screen to switch between landscape and portrait view mode (this benefit is actually a big disadvantage when I browse things while lying in bed, because it forces me to hold the iPod at uncomfortable and odd angles). Finally, if you double-tap on a column of text, the screen automatically zooms into that column to effectively use the small screen.
Some final notes: the shiny touch-screen on the iPod is ALWAYS smudged with fingerprints, whereas the Kindle screen is always clean (albeit dust). The iPod screen makes my eyes hurt in the dark, and after a long day of staring at computer monitors, while the Kindle is always the same brightness as the surrounding environment, and much less tiring on my eyes (but also requires a reading-light since there is no backlight).