Gabe, I think you're right about pretty much everything you said. I haven't been here for long enough to remember a voting system other than 1 - 10, either. But old comics and forum posts suggest that it was once -5 to +5, then went down entirely for a while, then came back in its present form.
Comics that were made during the -5 to +5 period shouldn't have an advantage over later ones, because not only could they only get half as many points in one shot then as they can now, they could also get points taken away. However, older comics from the 1 to 10 era should be doing better than newer ones. I've found that this is often the case, though not always. Sort the list by score and then see how many pages down from the top you have to go before you start getting significant numbers of strips from the last three or four days. In fact, recent strips in high places are a good sign someone's been cheating. I share DexX's suspicion that some third party may have promoted Fracture's strip to the top 10. It's not that the strip isn't funny, just that it's too recent.
I suspect that the more comics there are, the more pronounced this effect will be.
Sometimes it seems to me as if the randomizer is weighted so that it's more likely to display newer comics. No official word about this as far as I know.
I don't know why we don't use an average-rated system. Probably because it would be more work to code, and because we've been using totals since the beginning and now have no record of how many votes each strip has received. The -5 to +5 system sort of is average-based, though.
I think "Most Popular" means that those comics have been viewed more often than others. Putting those comics in a highly visible place only assures that they'll get viewed more often and thus will become even more popular. I remember seeing the list change once or twice, but not much.
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The what mentioned above is total fiction. Please don't take it seriously!