I agree with pretty much everything said so far. But want to add that the difference in sound actually goes beyond which strings are emphasized. A big part of the difference in sound is which strings are omitted in the up strum.
In basic rhythm guitar playing (which strumming usually is) our strumming serves to establish a certain rhythmic feel to the song. In most cases, the upstrokes are part of keeping a consistent rhythm and the consistency part is best accomplished by establishing a pendulum type movement with your wrist. Hitting the strings on the up strum is often a part of establishing the rhythm pattern and feel of many songs - in which case you will want to strum some strings on the up strum as well as the down strum.
When doing this type down-up strumming, the natural arc of your strum will result in you missing some of the bass strings on the upstroke. This is normal, acceptable and common. I find that I have to make a conscious effort to play the low E string or A string on an upstroke as part of a down-up strumming pattern. And if I do make this conscious effort, it disrupts the rhythmic pendulum action of my wrist.
There are certainly situations in some songs where an intentional full up strum is part of the arrangement (often a slower rake), but you really have to slightly alter your normal up-strum to accomplish this. I usually do this type intentional full up strum with more upward movement in my forearm as opposed to just the wrist.
So in most rhythmic strumming patterns, your up strum will miss the bass notes of the chord your are holding and thus will sound a little thinner for that reason alone (in addition to other reasons mentioned). In most cases the accent beats will be emphasized by using a down strum. In other words if your were counting One and Two and Three and Four and .... - the up-strums would be on the ands. That's why it's actually a good thing that the natural arc of an up-strum results in playing fewer strings. The exceptions require conscious thought and alteration in your normal strum.