Ok, your first question was what regulates expression of genes in some cells and not others: The key is promoter regions. Each gene (insulin, glucagon, etc.) has a promoter region that only allows it to be expressed in the "right" cells. So even though the DNA is present in every cell, expression is only turned on in appropriate cells where the right transcription factor "turns on" the gene and allows the DNA to be made into mRNA (and eventually into protein).
The rest of your question confuses me a bit...hopefully someone else can answer you. My understanding is not that the DNA/chromatin intself changes in a stem cells vs. a differentiated cell, but that the cell begins to have expression markers of different lineages turned on. People are working very hard to try and make differentiated cells behave like stem cells...just in the last couple weeks, some groups have said they were able to turn skin cells into cells that are "identical" to stem cells...you can see a "newsweek" story that mentions these papers here
http://www.msnbc.msn.com/id/19094606/site/newsweek/?from=rssand you should be able to find them on PubMed if you are interested in the details.
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