One example of a work that managed to find a good balance of pop culture references is the show Farscape. It used a ton of pop culture references, yet all were sufficiently well-known as to be familiar to just about any Westerner who wasn't living in a cave for the last fifty years, and well-established enough that they don't seem obscure or outdated even though the show ended a decade ago.
I think Farscape did a great job of having their cake and eating it too. John Crichton is a pop culture machine, throwing out references left and right, so American audiences immediately sympathize with him and laugh at his jokes. His companions are aliens from another galaxy, so all of his references are completely lost on them. Foreign audiences (or those just not as plugged in to pop culture) sympathize with his crew and their baffled reactions.
I read a book (part of the Laundry series by Charles Stross) where the main character says he was enjoying reading this book series about a wizard in modern-day Chicago. Doesn't call Harry out by name but it's pretty obvious what he's referring to. The same book has a cultist die via iPod commercial (which, interestingly, most of his British audience would not get). For something less mainstream like the Dresden Files, I'd go for an oblique reference. Maybe something like "I thought about waving my hands and shouting FUEGO but I didn't want to deal with the bill for property damage" or "I needed to think my way through this. Come up with something unexpected. Unfortunately, all I could think of was a polka-powered zombie t-rex. My brain must be on strike."