Medieval Manuscripts in Oxford Libraries is the online catalogue of western medieval manuscripts in the Bodleian Library and selected college libraries. It contains brief descriptions of every Bodleian manuscript, including links to images of the Summary and Quarto catalogue entries, and full descriptions of a growing number of Bodleian and college manuscripts, including most of those acquired by the Bodleian since 1916.
For more detail on the catalogue and advice on using it, see here.
The medievalist staff in the Library maintain a Zotero bibliography which records published references to Bodleian and other Oxford manuscripts. The great majority of the references have been converted from the bibliographical card index known as 'Bodley Refs.' The process of conversion is ongoing, and the bibliography currently covers works published between approximately 1992 and 2016.
For advice on using the bibliography, see here.