This post will grow over time, so check back from time to time, as I put the new update date in the title.
Do remember that most cold water viruses do not affect humans, however, the issue is that fish farms, due to their density of fish, cause mutations in viruses. There are also fungal and bacterial diseases in farmed fish, several dozen in total.
1. Google: fish farm diseases that infect humans and you will be reading for days: https://www.google.ca/search?hl=en&site=&source=hp&q=fish+farm+diseases+that+infect+humans&oq=fish+farm+diseases+that+infect+humans&gs_l=hp.4...421.6609.0.74220.127.116.11.0.0.0.269.3750.14j20j1.35.0...0.0.zV5g8os4OMk.
2. Kudoa septempunctata. This is not the Kudoa species that has been found in Marine Harvest BC farmed salmon. It is a relative, and has been shown to make more than 1300 people in Japan sick from eating raw fish. See: http://www.ncbi.nlm.nih.gov/pubmed/22281845.
3. Fish diseases that infect humans: http://mudiparofarms.com/?p=90.
4. Asian fish product diseases that infect humans. See this for liver flukes and trematodes: http://wwwnc.cdc.gov/eid/article/15/4/08-1147_article.htm.
5. A long list of diseases that fish transmit to humans: http://www.scribd.com/doc/3699145/Disease-Trasmitted-From-Fish-to-Human.Note that these are not necessarily from fish farms, just from fish.