Now, back to magnets. Using them as "unconventional batteries" is the entire point here, it's not like anyone's trying to create a "perpetuum mobile" here. The mechanical parts of the thing would wear out long before the magnets themselves would be significatly exhausted, anyways. If a PM motor would have to have its magnets changed every year to keep efficiency up, how would that be bad?
Magnets are
extremely inefficient for energy storage. Creating a magnet artificially takes a ridiculous amount of electrical energy (try hooking up a copper coil to a 9-volt, and try magnetizing a paperclip), and once you're actually extracting a non-negligible amount of power from the magnetic field the magnets weaken fairly quickly.
If you paid attention to the magnets your science teachers kept, you'd notice they had to pack them in a special way to prevent them from being demagnetized, even when they weren't doing any significant work.
Besides, you lose energy way too many times. You convert between states five times.
WhateverYouUseToGenerateElectricityInTheFirstPlace-> Electrical
Electrical -> Magnetic
Magnetic -> Mechanical
Mechanical -> Electrical
Electrical -> Mechanical.
Using magnets directly to drive an engine would be a horrible design nightmare (just off the top of my head: different power output based on how long you ran it, worries about other ferromagnetic influences, alignment of moving parts, inability to use magnetic alloys, large and bulky connections, inability to control rate of spin, low torque), so you'd have to run a generator with a spinning magnetic wheel. In addition, you'd have to watch to make sure the magnets don't get too hot or jolted around, as that demagnetizes them as well.
There's a reason they aren't used. The energy storage density is low, the power output is low, the efficiency is low, the array is delicate, and storage is a major hassle.
So, to round up the alternative energy list...
Hydrogen isn't easy to store at all. It's explosive, is the most readily diffusing gas, is a gas in the first place, and reacts with all sorts of things you don't want it to. I've seen some tentative progress with buckyballs that may make widespread and safe implementation possible in, say, twenty years. Before then, don't get your hopes up.
Biodeisel is actually a good idea, although the ridiculously cheap stuff people are making in their backyards isn't really that representative a sample (the supply of restaurants with free leftover cooking oil is fairly low). On the other hand, all you need to do to convert a diesel motor is put in biodiesel, drive ten miles, replace your filter with a new one, and off you go. Given that the USA is the world's largest producer of soybeans, their oil crisis may be resolved with soybean oil, although I don't know enough to say how much energy it costs to produce, and what output you'd get.
Ethanol is a bad idea as currently implemented, simply because corn isn't the best choice of crop. Algae might work, as could several other plants, but corn isn't ready yet.
There's no real reason to carry around water for fuel - all the designs I've seen involving it use hydrogen fuel cells, and make hydrogen from water. That's fine as far as it goes, but you're really just carrying around the water from your exhaust and using the hydrogen as your battery. The power has to come from elsewhere, like solar panels or the electrical grid.
Depending on how research goes, fusion seems like it could be a possibility for electrical power generation. Boron-based fusion looks promising since the radiation produced is minimal. The Bussard polywell design is interesting, but I would need someone with more technical knowledge than I to look it over.
Nuclear fission power is sadly underutilized everywhere except France. It's clean, it's safe, it's already here. Unfortunately, public perception is negative enough that self-proclaimed "environmentalists" can put a halt to projects by raising the nuclear bogeyman.
Natural gas is too cheap. So cheap it gets wasted at the well when the price drops too much. Better than releasing it into the air unburned, I admit (even worse for global warming then), but the development of some kind of small powerplant for the wells would eliminate a large amount of waste
Solar panels seem like a good idea, but they still have a lot to gain in efficiency before they arrive. The same can be said for wind power, but there's also the added worry about abuse of wind power causing undesirable climate change (extract enough energy from the weather, and I guarantee you'll see some effects). Hydroelectric dams cause small-to-medium earthquakes in the surrounding areas if they're large enough, and kill off river species.