Aside: it's looking like Lamarck was right.
One rather relevant example from a recent new scientist that, in rats, overweight dad rats had offspring who more likely to get diabetes.
I get the impression it's early days with all this stuff, but it's going to be interesting.
http://en.wikipedia.org/wiki/Epigenetics
http://www.sciencedaily.com/releases/2005/10/051026090636.ht...
Methylation of DNA tends to persist through cell division because there are enzymes which approximately copy over the methylation patterns during DNA replication. If some epigenetic changes happen in sperm or eggs, then some of this may be carried over to offspring. You're right that we're still in the early days of mapping this out and understanding it. Molecular biology is a crazy mess that makes the worst spaghetti code look downright reasonable. That's evolution for you....
This is an oversimplification, but imagine you have a sweater that you dye bright green. You then unravel it and use part of the yarn, along with yarn from another sweater, to knit a new sweater. Some of the new sweater will have the same physical change, the bright green dye, that the old sweater had.
Sure, but only cell#1 has the actual molecules from the parents.
Cell division requires that the DNA be replicated. What surprises me is that the replication step (apparently) preserves methylation. (If it didn't, there would be no observable epigenetic effect in the organism).
i.e. from an information perspective, the bits encoded in the DNA aren't don't just come from the sequence of bases, but also "out of band" data.
In it the authors discuss the evolution of the eukaryotic cell: a multi-part cell that evolved due to penetration or symbiosis of multiple organisms. Pretty much all complex life evolved out of eukaryotic cells. In particular the mitochondria that power your cells did not evolve from the same stuff that the rest of your cells did -- they were an addition later on.
Likewise, most of the genetic diff between us and Chimpanzees (or for that matter, blue green algae) are from external sources -- viruses and 'parasites'.
For that matter, 90% of the cells in your body are not genetically yours -- they are other microbes (though these account for only 10% of your body mass). If you are purged of these cells, you die. This lack of microbial transfer was one of the reasons suggested for why infant mortality was so high in the years when babies were isolated from their mothers and other human contact upon birth.