What about time and date formats? While some formats based on a single scalar value (e.g. Unixtime) are common in certain applications, the system most commonly used by humans to specify the time of day uses at least three different units (hours, minutes and seconds), with a conversion factor (60) that isn't a power of ten. The rules for calculating dates are even more complicated. Time zones complicate matters further; a single '%Y-%m-%d %H:%M:%S' string doesn't even unambiguously specify a point in time, unless one already knows what time zone the sender is using. From a purely algorithmical perspective, this is a really poor way of specifying a scalar (approximation; none of the systems mentioned deal with time dilation) value. While it encodes certain additional information (position of a planet relative to the local sun), it also makes performing arithmetic on datetimes a lot more difficult than it needs to be.
Today my coworker Marcello pointed out to me an interesting anti-majoritarian effect. There are three major interpretations of probability: the "subjective" view of probabilities as measuring the uncertainty of agents, the "propensity" view of probabilities as chances inherent within objects, and the "frequentist" view of probabilities as the limiting value of long-run frequencies. I was remarking on how odd it was that frequentism, the predominant view in mainstream statistics, is the worst of the three major alternatives (in my view, you have to presume either uncertainty or propensity in order to talk about the limiting frequency of events that have not yet happened).
And Marcello said something along the lines of, "Well, of course. If anything were worse than frequentism, it wouldn't be there." I said, "What?" And Marcello said, "Like the saying that Mac users have, 'If Macs really were worse than Windows PCs, no one would use them.'"
At this point the light bulb went on over my head - a fluorescent light bulb - and I understood what Marcello was saying: an alternative to frequentism that was even worse than frequentism would have dropped off the radar screens long ago. You can survive by being popular, or by being superior, but alternatives that are neither popular nor superior quickly go extinct.
I can personally testify that Dvorak seems to be much easier on the fingers than Qwerty - but this is not surprising, since if Dvorak really were inferior to Qwerty, it would soon cease to exist. (Yes, I am familiar with the controversy in this area - bear in mind that this is a politically charged topic since it has been used to make accusations of market failure. Nonetheless, my fingers now sweat less, my hands feel less tired, my carpal tunnel syndrome went away, and none of this is surprising because I can feel my fingers traveling shorter distances.)
In any case where you've got (1) a popularity effect (it's easier to use something other people are using) and (2) a most dominant alternative, plus a few smaller niche alternatives, then the most dominant alternative will probably be the worst of the lot - or at least strictly superior to none of the others.
Can anyone else think of examples from their experience where there are several major alternatives that you've heard of, and a popularity effect (which may be as simple as journal editors preferring well-known usages), and the most popular alternative seems to be noticeably the worst?
Addendum: Metahacker said of this hypothesis, "It's wrong, but only sometimes." Sounds about right to me.