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While I have not negotiated a publication agreement, I have published in open access journals where the author retains the copyright.
Open access publishing is a rapidly growing format that seems to work well, at least in my experience. Places like BioMed Central and the Directory of Open Access Journals are two open access publishing resources worth exploring.
Even the NIH is getting into the swing of it with their PubMed Central, though in many cases, there is a waiting period before the papers are free for viewing by the public. I do not know what their copyright policy is.