Interoperability of software is still a major issue. Not only closed systems do not play well with others, open systems sometimes—often—have the same problems with exchanging information. One that only plays well with others when forced to is, of course, our good friend Microsoft. Sometimes they pretend to play well, and other software developers must reverse-engineer the file formats to read and write data in a compatible format.
One minor annoyance is Microsoft Office’s clip-art bundle file format that is not supported (at the time of writing, anyway) by Open Office. This means that you can download clip-art for your presentation only to discover that they are perfectly useless. Or, you can take 10 minutes and look at what the bundles actually contains!