Element shortages are in the news these days. The US has been talking about shutting down its strategic helium reserve, and there are plenty of helium customers worried about the prospect. The price of liquid helium, not a commodity that you usually hear quoted on the afternoon financial report, has apparently more than tripled in the last year.
I think that this is more of a gap problem than a running-out-of-helium one, though. There's still a lot of helium in the world, and the natural gas boom of recent years has made even more of it potentially available. Trapping it, though, is not cheap - this is something that has to be done on a large scale to work at all, and substantial investment is needed. Air Liquide has a liquefaction plant starting up in Qatar, but that won't be running at full capacity for a while yet, it appears. I think, though, that this plant and other such efforts will end up providing enough helium for industry and research, at a price. We aren't running out of helium, but the cheap helium is going to be in short supply for a few years.
At the other end of the periodic table, though, it looks like we really are running out of plutonium-238. One's first impulse is to say "Good!", because the existing stockpiles are largely the result of nuclear weapons production in years past. But it's an excellent material to power radiothermal generators, since it has a reasonable half-life (87.7 years), a high decay energy, and is an alpha emitter (thus needing less heavy shielding). Note this picture of a pellet of the oxide glowing under its own heat. There are a number of proposed deep space missions that will only launch if they can use Pu-238 that no one seems to have. Russia sold about 16 kilos to the US in the early 1990s, but just a few years ago they backed out of a deal for another 10. No one's sure - or no one's saying - if that's because they would rather hold on to it themselves, or if they don't really have that amount left any more. To give you an idea, the proposed Europa mission to Jupiter would need about 22 kilos.
There are efforts to restart Pu-238 production, but as you would imagine, this is not the work of a moment. As opposed to helium, which is sitting around in natural gas underground, you're not going to be mining any plutonium. It has to be made from neptunium-237, which you only get from spent nuclear fuel rods, and the process is expensive, no fun, and hot as blazes in every sense of the word. Even if the proposed restart gets going, it'll only produce about 1.5kg per year. So if you have any plans that involve large amounts of plutonium - and they'd better involve space exploration, dude - you should take this into account.