With the explosion of the number of ontologies and vocabularies available in the semantic web, ontology libraries and repositories are mandatory to find and use them. Their functionalities span from simple ontology listing with metadata description to rich platforms offering various advanced ontology-based services: browse, search, visualization, metrics, annotation, recommendation, data access, etc. Studying ontology repositories opens then a wide spectrum of informatics research questions in areas such as knowledge representation, semantic web, data integration, natural language processing, ontology alignment and more. Ontology repositories are usually developed to address certain needs and communities. BioPortal, the ontology repository built by the US National Center for Biomedical Ontologies is the most important resource in biomedicine. It relies on a domain independent open technology that we have contributed to build (at Stanford) and extensively reused and extended for our research (at University of Montpellier) and applications to biomedicine and agronomy. In this manuscript, we present and discuss six high level challenges for ontology repositories and services: (i) standardize and extend metadata used to describe ontologies and use these metadata to facilitate ontology evaluation, identification and selection; (ii) multilingualism, which requires rethinking ontology repositories to embrace (and encourage) the multilingual semantic web; (iii) all issues related to ontology alignment, not just the automatic generation of mappings, but also their extraction, storage, validation, etc., (iv) the design of better and new generic ontology-based methods especially for processing free text data, (v) the use of ontologies for semantic annotations & linked data; and finally, (vi) scalability & interoperability of the different semantic resources management platforms. For each challenge, we describe and point to results obtained in the context of our ontology repository projects over the last 12-years, especially the NCBO, SIFR, PractiKPharma and AgroPortal projects. We believe our results illustrate potential solutions to move forward in this domain of research.