I am doing Hoechst stain to detect apoptosis in my cells. Apoptotic cells have condensed chromatin which would be stained brighter than that of normal healthy cells. However, when cells undergo mitosis, their chromatin also condensed, So how do we differentiate the condensation and more brightly stained chromatin between apoptotic or mitotic cells? Flow cytometry assays also show that about half of the cell population are in G2/M arrest. so, in this case, is Hoechst staining a good way to detect apoptosis?

Sadly, Hoechst staining remains a rather subjective and non-quantitative staining / apoptosis assay. If you do not have any cell number and time limitations- which will be true of most cell lines(adherent or suspension) and some primary cultures too, your best bet is to have the cell cycle PI staining in conjunction with non-permeant-PI/Annexin-FITC in a FACS assay (or similar combination - there are 4 popular combinations of Annexin conjugate/late apoptosis/necrosis markers available that I know of).
The advantage of Flow cytometry is that its both objective and quantitative- which is very important for cell death assays, plus it deals with single cells in a population.

Apoptosis stage markers in addition to annexin/PI will include permeabilized PI (FACS) or EtBr (Agarose gel EP) for DNA fragmentation,
mitochondrial potential transformations with JC-1 (confocal/fl microscopy and FACS),
PARP cleavage and caspase activation (lots of colorimetric/fluorometric/ELISA/IHC/FACS kits are available, or you can just get the Abs and set up your own assay),
the FLICA/FLIVO system (do a search for the company here on Solutions search - above)
lactate dehydrogenase release (sometimes crude, but works well for some cell types: did not work very well for T cells in my lab)
etc.
Other than LDH, all the rest have worked well for me with PBMCs/purified T cells.
Hope this helps!
-sam

thank you !