My 1996 Honda Civic, for example, has a tank that will hold 11.9 gallons (according to the User Manual specs). Yet, I tend to fill up with just 8 gallons when my needle reaches E. Since I average 34 MPG (according to Fuelly), I should theoretically travel 405 miles from a full tank. I'm tempted to drive 400 miles before a fuel up. Or is my math somehow wrong- since I never filled up from a near empty tank?
It may be due to your needle dipping to E before you actually run out of gas. I'd not recommend pushing to 400 miles, as that last 5 miles could cause an issue if you're hunting for a gas station.
On top of that, I know with my GA, if I run out of gas, I'm pretty much guaranteed to be required to purchase a new fuel pump. Gets ugly.
I'd recommend just staying the course. Yes, you may have to fill up more often, but in the long run, you'll save on maintenance to the car. True, you may lose in MPG with carrying more fuel all the time (Less gas, less weight to haul around) but, I'd rather do that than be out a car due to repairs.
Another concern is sediment in the tank. When you run a tank totally empty or nearly empty the percentage of sediment in the fuel increases dramatically. If that sediment is picked up by the fuel pump it will travel to the fuel filters, most modern Honda's have a primary fuel filter and a secondary one. If those filters clog you'll have to replace them and even worse if some of that sediment gets through them you could clog your fuel injectors which can be costly to repair or replace.
Finally if you decide to go ahead and see how much fuel is left after you hit empty on the gauge (BTW, you don't mention if you have a gas light on your dashboard, on my Acura that is supposed to illuminate when there is only 2 gallons remaining in the tank) bring a jerry jug with a gallon or two of gasoline in it so that if you do run totally out you have that to get you back on the road and to the nearest gas station.
I'm pretty sure that most cars don't actually hold the rated fuel capacity. The fuel pump generally shuts off once pressure inside the tank reaches a certain point, allowing some space for fuel vapors inside the tank. If you top or your tank several times, very slowly, you might be able to overcome this, but it'll probably screw up your evaporative emission control system and wouldn't really have any benefits, so I wouldn't recommend it. In addition, the fuel pickup may not be at the absolute lowest point in the tank, resulting in the car not being able to pump fuel to the engine while there is still some fuel left in the car. This helps to keep sedimentary buildup and water out of your fuel system, although is not guaranteed to do so, so don't run your tank all the way down.
There is a website that tracks how many miles people can drive their cars after E if you want to know. In cold weather this is useful information, but that extra fuel usually cools the electric fuel pump. People who run it low increase their risk of burning up said fuel pump (though the fuel running through it should cool it in adequately reasonable weather. Sediment has not been much of a problem since the advent of plastic gas tanks. My Miata specs out at 12.6 gal. On an adventure I have gone another 20 miles past E, but still only put 11.8 in to "fill" it. (you really don't ever want to FILL your tank unless you are getting back onto the road immediately in freezing weather; otherwise, expansion of the fuel as it warms might cause overflow.)
Also, if you've seen the shapes of fuel tanks these days you may be aware that many of them have places that will hold a bubble until you start driving (engineering's protection for those who want to fill the tank all the way?).
In cars the fuel is drawn from the bottom of the tank. If there's sediment, it's going to be drawn in whether you run your tank dry or not.
That's actually a good thing. It keeps the sediment from just building up and building up until one day you really do need to use that last drop of fuel and it's so full of crap it doesn't burn or clogs the fuel lines or something.
Motorcyclists with a reserve tank have to be more careful about it, since under normal operation the fuel is not drawn from quite the bottom of the tank.
The other thing I have noticed is that after the auto shut off on the pump clicks off I can put in another 2+ gallons of gas. I just slow the pump way down and fill it until I see the gas just start to leak out. The way I look at it, I no longer have to wonder if one auto shutoff is different from another. I just always fill my tank until the gas starts to seep out. And surprisingly it is usually at least another 2 gallons.