This is the list with dupes, but most of them are mpi.eclass related.

dev-ml/ocamlgraph
  Portage: 0.99b
  Overlay: 1.2
dev-python/pytables
  Portage: 2.1.2
  Overlay: 2.2_rc2
dev-tcltk/togl
  Portage: 2.0-r1
  Overlay: 1.7-r1
sci-biology/mrbayes
  Portage: 3.1.2
  Overlay: 3.1.2-r1
sci-chemistry/burrow-owl
  Portage: 1.4
  Overlay: 1.4 9999_pre15
sci-chemistry/coot
  Portage: 0.6.1 0.6
  Overlay: 9999
sci-chemistry/gromacs
  Portage: 3.3.1-r1 3.3.3 4.0.4 4.0.5 4.0.7-r3
  Overlay: 4.0.9999 9999
sci-chemistry/jmol
  Portage: 11.0.3-r1
  Overlay: 11.6
sci-chemistry/pymol
  Portage: 0.99_rc10 1.2.3-r1 1.3.0
  Overlay: 9999
sci-chemistry/pymol-apbs-plugin
  Portage: 0_p15 0_p18
  Overlay: 9999
sci-geosciences/qgis
  Portage: 1.4.0 1.4.0-r1
  Overlay: 9999
sci-libs/hdf5
  Portage: 1.6.4 1.8.4-r1 1.8.5
  Overlay: 1.8.4-r2
sci-libs/starparse
  Portage: 1.0-r1
  Overlay: 1.0 9999 9999_pre10
sci-mathematics/maxima
  Portage: 5.18.1 5.19.2 5.20.1-r2 5.21.1-r1
  Overlay: 5.20.1-r3
sci-mathematics/scilab
  Portage: 4.1.2-r1 4.1.2-r2
  Overlay: 5.2.1
sci-visualization/gnuplot
  Portage: 4.2.6 4.2.6-r1 4.4.0
  Overlay: 4.4.9999 4.5.9999
sci-visualization/paraview
  Portage: 3.6.1 3.6.1-r1 3.6.2
  Overlay: 3.8.0
sys-cluster/hpl
  Portage: 2.0
  Overlay: 2.0
sys-cluster/lam-mpi
  Portage: 7.1.4-r1
  Overlay: 7.1.4-r1
sys-cluster/mpe2
  Portage: 1.0.6_p1
  Overlay: 1.0.6_p1
sys-cluster/mpich2
  Portage: 1.0.8 1.1.1_p1 1.2.1 1.2.1_p1 1.2
  Overlay: 1.1.1_p1 1.2.1 1.2.1_p1
sys-cluster/openmpi
  Portage: 1.4.1 1.4.2
  Overlay: 1.4.2-r1