With an individual modem/router, I have more control over my network. Also, if I change ISP's (which, I have done recently), I only have to set the modem up to work with the pre-existing router. I don't have to go reconfigure all the laptops and my daughter's Nook to get them on to the new network like I would if I had a modem/router combo.
Plus, if your internet is down but a friend comes over and y'all wanna co-op some games together (like Diablo II LOD, or C&C Generals Zero Hour
) the modem/router combo doesn't always let them on the network if internet is down. With a separate router/modem, the router doesn't even care about internet access.
On paper, the difference really should be minimal, but in practice the modem/router combos just suck imo. Especially for wireless access. Most combo devices have extremely poor wireless signal and almost zero flexibility in customizing the signal strength.
This is all based off of my personal experience helping others fix their computers and home networks over the last 12 years or so.