Software bugs are a fact of life, but in general, applications improve with each release. You can avoid, or solve, many maintenance problems simply by making sure you have the latest version of every program installed.
In some cases, getting the latest version of a program means spending hundreds of dollars on a major upgrade. In cases where you can't afford the absolutely latest version, you should at least install the latest free update you can find. This may require some searching on the company's Web site; earlier updates may not be featured as prominently as the most recent update.
Because Software Update handles only Apple software, any other developer wanting to offer similar capabilities must devise a separate update mechanism. Happily, almost every major application (and a good percentage of minor ones) contains some sort of software update feature. Unhappily, they don't all work the same way. Some of them check for updates on a schedule, while others don'tand of those that do, not all have this feature turned on initially. Some programs can download and install new versions of themselves automatically, while others simply download a disk image and expect you to open it and run the installer yourself; still others do nothing but open a Web page with links to updates you can download manually.
In an ideal world, updates would require no intervention other than a single click to confirm that you're aware of, and approve of, the installation; everything else would happen automagically. Because only a few applications currently offer that level of automation, though, you may have to perform some extra steps.
I describe how to handle ongoing updates ahead. For now, do just two things:
Some applications check for updates every time you launch them, and display an intrusive alert after each check just to tell you that no updates are available. Ugh! An alert of that sort should appear only after a manual check for updates. In such cases, I either turn off automatic checking or change it to a weekly or monthly check.