How much do you want to spend? The automatic, whole house systems are really nice but will run you big bucks. The manual, run extension cords plan is cheap but a PITA...then there is the whole gamut in between.
There are also less-than-safe ways of running a generator into the house, called back-feeding, but you could really hurt/kill yourself or someone else (like a guy working on your powerlines). I don't recommend them.
I have a hybrid system that takes advantage of a second circuit panel box that I had to have installed when I moved in. I had an electrician rewire the system to put all the circuits I wanted to be run by a generator put into the second box. The second box is energized by a circuit breaker that allows you to shut off power coming in from the first box (main), and it also has a circuit breaker that controls a 30A plug in the garage. The generator plugs into that inlet in the garage.
Now here is the critical part. The electrician installed a restraint bar that isolates the second box from the first box when the circuit going to the generator plug is open. Either the second box is getting power from the generator and not from the first box/main (when the power is out), or it is getting power from the first box/main, but never both. This prevents you from inadvertently back-feeding generator power back out the grid. The bar also prevents power from going out to the generator plug when the main power is on.
This is essentially what a transfer box does, and you'd probably go that route if you don't already have a second box. But putting in a second box may be a cheaper alternative. I'm adding all of these details about my system as another way to skin a cat. I offer it up as something to discuss with your electrician....informed consumer and all that.