I hate journal articles. I don't hate publishing research. Journal articles are the standard means of publicly communicating research findings to the rest of the scientific community and I don't hate that either. What I hate is the fact that I need to keep track of literally hundreds of 10-20 page documents - it's a logistical nightmare. My undergraduate adviser accomplished this with a pair of 5 drawer filing cabinets. My current adviser has dozens of boxes of reprints sitting on shelves in our computing lab. I generally prefer electronic versions for storage purposes, but that becomes a mess when getting papers from ADS, the arXiv, and individual journal websites - all of which use their own convention for filenames. I hate the piles of papers, either physical or electronic, that result from journal articles.
Papers. First a couple of disclaimers - it is not freely available (it costs $25.20 for students, $42 for everyone else), it only works for Mac OS X, and it's really designed for people in biological sciences, so it doesn't integrate as well with the arXiv as I would like. Also since the software is developed by a small company (6 people, some of whom are also full-time scientists), upgrades and bug-fixes are often unpredictable.
Now that I've got the negative stuff out of the way, let's talk about why I'm writing this post. The bottom line is that Papers saves me time trying to find papers I want and allows me to effectively carry my entire library of journal articles with me wherever I take my laptop. On top of that, Papers can extract bibliographic information from PDF files and then export it in BibTex format, allowing me to easily create reference lists for papers. On top of all that, it provides a nice front-end portal to almost all of the major databases like NASA ADS, the arXiv, Google Scholar, and more to provide useful features. Let's say, for example, I want to know if one of the leading dynamo theorists and perhaps the most prodigious writers of journal articles in astrophysics (13 peer-reviewed journal articles so far this year) Axel Brandenburg has published anything new. Papers automatically interfaces with ADS (or another database of your choosing) and downloads the titles and bibliographic references to all of recent entries for all of the authors in my database. Here's a screen shot to illustrate my example and to generally show how spiffy Papers looks (click to embiggen):
The software is also easy to use as a PDF reader with note-taking feature. I regularly use it to read new articles on my bus rides to and from campus. They even have a new version for the iPad that allows you to read and annotate PDF's on Apple's latest wonder. If anyone would like to send me an iPad I'd be happy to write a review on that feature as well.
So if you hate piles of paper on your desk or trying to organized PDF's on your hard drive and happen to use a Mac, check it out. It's not a perfect solution, but it is the best thing I've found to alleviate my hatred of journal articles yet.