Assume that time is never ending.
Then, assume that “souls” exist which are also never ending.
Regardless of how long a soul spends doing whatever, if after that at any point it switches over to one activity for the rest of time, be that activity burning in hell or having a nice time in heaven, eventually the amount of time spent at the eternal activity will overwhelm all of the previous time until the previous time can have no significance. The time spent on earth will be 0.0000% of the time spend being rewarded/punished for it, to any precision you desire.
This is just a way of saying that eternity is a very very long time. 
Also, it brings into serious doubt the significance of earthly deeds. Any act carried out on earth cannot have the significance to earn either eternal suffering or eternal happiness. This has already been pointed out, I’m just including it for completeness.
The only rational reason I can think of for an eternal judgement system is if the “trial period” of the earthly life is meant to demonstrate which punishment you inherently deserved anyway. Perhaps some souls are worthy of damnation, and some are worthy of bliss, and the earth life is meant only as a 100% effective demonstration of which is which. The sins were finite acts, of literally no significance in an eternal scheme, but they could be a demonstrative litmus test for the nature of the soul, which is as eternal as the punishment/reward that it naturally deserves.
Assuming that this is right, the fact that God is doing a demonstrative test upon the already-existant characters of our souls could be justified by two reasons that I can think of: He didn’t know himself which souls were inherently worth of salvation before the test, or he did know and ran the test merely to demonstrate to the souls why they ended up where they did.
(How contradictory is all this with scripture, out of curiousity?)
This sort of binary selection scheme always seemed a bit harsh to me; there’s some bar and if you don’t clear it, hot feet for you. A continuous spectrum of reward/punishment seems a bit more fair. It’s interesting to note that the mormons (tCoJCotLDS, more accurately) assert that just such a continuous spectum exists, divided into four major categories. Okay, of the four categories only the top one is explicitly described as being a continuous spectrum, but the others are not specifically described as being otherwise. [/interesting note]
Before anybody gives my notions too much credence, you should note that they don’t describe an all-knowing, all-powerful, all-loving god. So you may want to look for alternative explanations than my reasoning if you wish to continue to entertain that particular fantasy.
By my reasoning, all the people who ain’t going to heaven were made that way. Earthy actions are indicators of eternal flaws, and not punishable in and of themselves. A God that would intentionally create souls headed by nature for eternal punishment indicates to me that either he didn’t quite know what he was making at the time, that he knew that there would be flawed souls made but couldn’t achive 100% production within his desired tolerance regardless of effort on his part, or that he’s a sick bastard who wanted to make sure that a few things didn’t cross the bar so he could watch them burn (maybe to keep the passing souls in line). So, pick one that he isn’t: all-knowing, all-powerful, or all-loving.
And the fact that he doesn’t merely show mercy and destroy the below-par souls when they have been shown to be such would indicate that either God is a sick bastard who likes seeing people burn, or that he can’t destroy souls that currently exist. So, pick one that he isn’t: all-loving or all-powerful.
I’m okay with an all-loving god whose knowledge and powers are imperfect regarding the manipulation of matter that is as eternal as he is. I won’t respect a God that burns people for fun, though. YMMV.