A given data element in the Workbench can contain different types of data. This is reflected when exporting data, as the choice of different export formats can lead to the extraction of some parts of that data object rather than others. The part of the data exported reflects the type of data a given format can support. As a simple example, if you export the results of an alignment to Annotation CSV format, you will get just the annotation information. If you exported to Fasta alignment format, you would get the aligned sequences in fasta format, but no annotations.
The CLC format holds all the information for a given data object. Thus if you plan to share the data with colleagues who also have a CLC Workbench or you are communicating with the QIAGEN Bioinformatics Technical Service team and you wish to share the data from within the Workbench, exporting to CLC format is usually the best choice as all information associated with that data object in your Workbench will then be available to the other person who imports that data.
If you are planning to share your data with someone who does not have access to a CLC Workbench, then you will wish to export to another data format. Specifically, one they can use with the software they are working with.