This is a complex and multi-faceted issue. The answer depends on the audience, who have varying degrees of a) knowledge in the domain, b) technical background, c) awareness of what the ontology is for and d) need to directly work with the ontology.
For everyone, and especially non-technical people, it is important for there to be natural language comments explaining the meaning of the concepts. It is helpful to have an overview of the ontology which has only the top few dozen classes and relationships (like a UML class diagram). It is good to have HTML documents that can be automatically generated from various tools. It should be possible to seamlessly move between levels of detail from the very general to the very specific ban back. Ideally, you want to have different layouts automatically created and tailored to different circumstances. There are many visualization tools available to help with some of these things, but much more remains to be done.
For the very technical individuals, who will be using the ontology on a day to day basis, it is important to be able to locate concepts that are similar to what they have in mind. For this, it helps to have the ontology classes and properties organized into a small number of disjoint hierarchies.
