There was a time when Mac owners scoffed at their PC-loving counterparts, who had to pore over paper manuals to grok the essentials of a software program before they tried to use it.
When graphical user interfaces were introduced, a lot of focus was on making software intuitive and easy to use. There were also hardware constraints -- not much CPU power or memory, minimal storage, low-resolution displays -- that forced applications to be simple by design. Modern applications, whether on the desktop or on mobile, have a lot more room to maneuver, and consequently may arrive with a much steeper learning curve
While your average iOS app may seem simple enough, quite often there are bells and whistles you might not know about. iPad apps may use the increased screen real estate to add more (and more obscure) options, and Mac or web applications can be far more complex than anything available on mobile platforms.
While it might seem like cheap advice to "read the manual," I find very few people actually do. There's an entire industry built around learning software tools, like the Take Control series, which I find immensely helpful. Granted, most software manuals are written in plodding, feature by feature style and not as entertaining "here's how you solve this problem" books, but even that dry documentation can be vital to your efficacy when using the software.
When I started using iBank, shortly after its debut, I was lured in by its accessible design. "This seems simple enough," I said as I started entering transactions. Over time it became apparent that I had barely scratched the surface of iBank's functionality. I eventually gave up on the program -- only to return over a year later, armed with more clues. This time I read the manual, in no small part because almost every question I looked up on the IGG Software Knowledgebase had an answer in the manual.
Another example: Productivity software. While applications like Things are simple enough, there's often a lot of functionality hidden in the manual. You may not understand how to tap into these features if you're just reading "This does that" in the documentation. This is where additional help may be required.
In my case, for task management I use OmniFocus (after trying every other "to do" application under the sun). OmniFocus isn't a simple list maker; it is a powerful database which can help you sort through mountains of tasks to allow you to focus on what exactly needs to be done next. You could likely spend days reading the manual and still come away with the "what now?" feeling. You could buy a book, but sometimes books on niche products turn out more like dry manuals. There's another answer, however.
For deeper, more powerful applications, I recommend paying for additional learning materials. I bought an excellent book on DEVONThink Pro from Take Control and I no longer feel overwhelmed by the powerful software. For OmniFocus, I knew I needed to use it better, so I upped the ante and bought into the Asian Efficiency series of posts on using OmniFocus. Take Control books are great, but (for me) sometimes the low cost can cause a lack of motivation. Asian Efficiency is more like an online course, and the cost is much higher than just a book. It's a powerful motivator to know you're wasting more than an evening of poker's amount of money with a course if you ignore it. This goes double for any app that's crucial to your business workflow; if you're earning your rent with Adobe's CS suite, don't stint on the training or courseware as you move from CS 5 to CS6. The hour you save searching for that missing dialog box or hidden feature might be billable.
We're starting to see some really amazing ebooks arrive on the iBookstore, too. These leverage all the multimedia functions in iBooks and if you're a visual learner, they can be vastly more effective than reading text alone. A great example is Markdown by David Sparks and Eddie Smith (our review here). By using video and audio in addition to text, there's almost no chance you'll walk away scratching your head. The downside is these media-enabled iBooks will quickly fill up your iPad's storage.
I also recommend going to focused conferences, or events like Macworld/iWorld, where there are sessions aplenty on various software packages and workflows (several TUAW folks have given talks at Macworld). Often these give you a bigger picture and show you how to integrate multiple tools into a consistent workflow. You'll also have the opportunity to ask questions of speakers and attendees, and this can often be the most helpful thing of all as you share tips and tricks and learn what matters most to you.
Finally, don't be afraid to seek out a guru who knows the app backwards and forwards. Many app experts share their tips and training suggestions on Twitter, Facebook or Google Plus, or on application-specific forums hosted by the developer or third-parties. Be polite, show that you've done your legwork first (if the question could have been answered by a fifteen-second scan of the manual, it's not a good use of your time or the guru's wisdom), and you might be able to draw on some help from above.