Several documentations tools support generating bibliographies and citation markers. For example, the Sandcastle Help File Builder allows defining <reference>s and referring to them by <cite> MAML tags. R Markdown supports many bibliography formats, including BibTeX and respects citations styles when exporting pdfs with Pandoc.
Is there any way to place references into Scaladoc comments? Best I could think about is including the BibTeX entry as verbatim {{{ }}} code, which is fine where a class or method is based on a whole single paper. However, referring to specific pages or figures (i.e. this method implements the pseudocode from p.26, Fig. 3.a of so-and-so) is awkward this way. I would very much prefer a single .bib file per project and \cite tags.