BibLaTeX can be used as an alternative to BibTeX for handling bibliographies.
BibLaTeX-support in TeXlipse is activated simply by putting
  \usepackage[your biblatex options]{biblatex} in the
  preamble of your document. Currently TeXlipse can make use of the backends
  BibTeX and Biber. BibTeX is the default
  backend for BibLaTeX; Biber is however by now the recommended standard.
  You can switch to Biber by including backend=biber in your
  BibLaTeX options.
Before you use BibLaTeX, please make sure that the backend of your
  choice (Biber or BibTeX) is installed and
  set up in the Builder Settings
  (Texlipse > Builder Settings).
  If you have been updating from an earlier version of TeXlipse, we also
  recommend adding the extensions .bcf and .run.xml
  to the temporary files extension list in the preferences Texlipse >
  Builder Settings > Latex Temp Files.