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Hindawi are a large CC-BY publisher based in Egypt, their XML corpus can be retreived from http://www.hindawi.com/corpus/
We have a bunch of well documented APIs, and support content negotation on our articels to return markdown. Our main rest api is built on top of fluidinfo. We have also just launced lens.elifesciences.org, and the front end and XML -> JSON converter can be found here and here. We are also experimenting with workflow systems in Amazon, you can find that proejct here.
http://isitopenaccess.org/ is a tool that will tell you if a single doi is open access or not. It's still under development, but here is a component that might be interesting.
The Altmetric API provides access to mentions of scholarly works on social media sites, scholarly bookmarking services and in science news outlets. A free key has been generated for use on the day to alleviate rate limiting.
Crossref have many apis, ones of iterest for this hackathon might include the their search api, or any of the many items in their labe.
Search the fulltext content of all PLOS articles, including search in specific sections (e.g. financial disclosure or materials_and_methods). The web interface is here, available fields in the API are listed here, and an R package is available.
http://www.ncbi.nlm.nih.gov/books/NBK25500/
Retrieve identifiers of articles that match search criteria.
Fetch full records
http://europepmc.org/RestfulWebService
http://europepmc.org/FtpSite - FTP archive of OA PMC articles
https://github.com/dasmoth/dalliance/ - a genome browser in javascript
http://www.ebi.ac.uk/Tools/biojs/registry/ - a registry of javascript visualisation tools for biological data
http://spectrumviewer.org/index.html - a javascript viewer for spectra
http://raphaeljs.com/ - one of the two best javascript visualisation libraries
http://d3js.org/ - the other best javascript visualisation library
https://gephi.org/ - display graphs, kinda like photshop for graphs, very cool.