My absolute favorite "Dean with kids" story is the currently ongoing WIP "The Wellspring" by the supremely talented scourgeofeurope. You can find the ninth and most recent chapter at http://scourgeofeurope.livejournal.com/24822.html , which also contains links in it to each of the other chapters. It's a crossover with Dark Angel wherein Sam and Dean come across a nine year old Alec and chaos generally ensues. It's got perfect characterization for everyone involved though and an absolutely lovely portrayal of Dean as he starts to take on more and more of a paternal role.