Digging through the literature, I've compiled a list of possible markers for various cell types, which I'll publish here for the benefit of any scientists who use anonymous blogs as their preferred information source, and the annoyance of any random passersby who couldn't give a damn about gastrulation.
primordial germ cell: ckit
trophectoderm: cdx2
trophectoderm: esxl1
trophectoderm: hcg
trophectoderm: krt18
trophectoderm: psg3
trophectoderm: sfxn5
amniotic epithelial cells: fgf4
amniotic epithelial cells: oct3/4 (pou5f1)*
amniotic epithelial cells: rex1
amniotic epithelial cells: sox2*
amniotic epithelial cells: ssea4*
embryonic stem: bmp4
embryonic stem: cripto
embryonic stem: dax1
embryonic stem: ecat1
embryonic stem: eras
embryonic stem: esg1
embryonic stem: fbx15
embryonic stem: fgf4
embryonic stem: gbx2
embryonic stem: gdf3
embryonic stem: klf4
embryonic stem: nanog
embryonic stem: oct3/4 (pou5f1)*
embryonic stem: rex1
embryonic stem: slc2a3
embryonic stem: sox2*
embryonic stem: stat3
embryonic stem: tert*
embryonic stem: utf1
embryonic stem: zfp296
gastrulation: cer
gastrulation: foxa2
epiblast/primitive ectoderm: e-cadherin**
epiblast/primitive ectoderm: not1
endoderm: afp
endoderm: atbf1
endoderm: gata4
endoderm: gata6
endoderm: hnf4
endoderm: ifabp
endoderm: onecut1
mesoderm: bmp4
mesoderm: eomes
mesoderm: hand1
mesoderm: lhx1
mesoderm: myf5
mesoderm: myod
ectoderm: cytokeratin
ectoderm: fgf5
ectoderm: hoxb1
ectoderm: lhx5
ectoderm: mash1
ectoderm: meis1
ectoderm: otx1
neuroectoderm: hesx1
neuroectoderm: musashi
neuroectoderm: ncam
neuroectoderm: nestin
neuroectoderm: neurod1
neuroectoderm: pax6**
neural tube: sox1
epithelium: collagen IV
epithelium: lamininb1
neural stem cells: bmp2
neural stem cells: cd133
neural stem cells: cd29
neural stem cells: cntf
neural stem cells: emx2
neural stem cells: isl1
neural stem cells: nanos1
neural stem cells: nestin
neural stem cells: shh
neural stem cells: sox2
glia: gfap
oligodendrocyte: cnp
neuron: mbp
hematopoietic stem cell: cd34
cardiomyocytes: mlc2a
cardiomyocytes: mlc2v
photoreceptor precursor: nrl
*Redundant. Known to stain two distinct cell types.
**I've found these to be redundant.
干細胞相關儀器試劑耗材