The results of the deep HI survey AGES are presented for two regions in the Virgo Cluster. Covering a total of 15 square degrees to a sensitivity of 0.6 mJy/beam, 73 objects are detected within the cluster, with 109 detections in the background. A new automatic extractor is described which gives greater completeness and reliability than previous methods. The majority of the cluster detections are associated with galaxies previously identified in the optical Virgo Cluster Catalogue, but nearly 30% of the cluster detections are new objects below the VCC completeness limit. Their optical and HI characteristics are described. No definite optically dark galaxies are identified, however 4 intriguing candidates are reported. All have possible optical counterparts but these are extremely faint, and their HI velocity widths appear inconsistent for such objects when compared to the more certain associations. The likelyhood that these are really dark galaxies is discussed, but further observations are required for a more definitive analysis. Cluster galaxies are found to be significantly HI deficient but it is not clear where their missing gas has gone. An automated algorithm is described to try to recover faint extended HI features, but no detections are made. The HI may be ionised by the intracluster medium or the sensitivity of the survey insufficient - the relative merits of these views are assessed. A small fraction (10%) of the early-type galaxies identified in the VCC are detected in HI. Evidence that some of these are morphologically evolving via gas loss, while others are recent additions to the cluster as yet unaffected by their new environment, is discussed. I also compare and contrast the two separate areas studied, describe the cluster's HI mass-function from AGES and other surveys, and discuss the overall influence of the cluster environment on galaxy properties.