Man, I have so not been storing mine optimally. But then I think...
I'd say that if you'd like them available for use in the next 3 months or so, just store them fully charged. For anything you have in rotation, fully charged is fine.
It's not uncommon to be rotating three batteries or packs, so that even with one in the charger, you still have one in use, and one ready for use. It's also not uncommon to have some batteries that are sitting on a shelf, ready to replace one of those three batteries/sets, when they're ready for retirement. Those shelf-batteries are the ones you might not want to fully charge. Sure, you'd have to charge it up first, but getting it from the shelf beats waiting for it to come in the mail.
Personally I like the idea of having a rotation of three batteries/sets, as well as 3-4 available for replacing those.
I've yet to come across any paper describing a staggering difference in leaving it stored fully charged, as opposed to at a lower charge. Sure, there is a difference, but it's not so huge that I'd like to recommend everyone run out and get fancy (expensive) chargers to charge/discharge their batteries to a specific state of charge.
There's also a couple of issues that are often confused with the storage-question;
One is that there's a recommendation for storing at 30% (number varies a bit) for *shipping*. A battery charged to 30% is actually safer to ship than a fully charged one. If you have an aircraft filled up with LiIons, you want that safety margin on your side.
The other is that there can be a significant difference in how many cycles a cell can take, based on how high you charge it, and how low you deplete it. If a specific cell would survive full discharge and full charge 500 times, the same cell might be able to go from 60% to 30% and back up a total of 2000 times. There's an important key point here though; With those numbers, you extract 3 times as much energy from the full discharge/charge, as compared to the other. That means three times as many charge-cycles, and that "eats up" most of the quadrupling in the number of cycles. Okay, so you get 4 times as many cycles, but that's not all that important when you'd have to use three times as many cycles for the same amount of work. There's a gain to be had sure, but it usually doesn't make too much sense to go for it. You'd also be moving wear to the light and charger, and I'd much rather wear a $5 battery that's easily replaceable, than a $50 light I might be attached to. These things are important for engineering tasks (you could increase a battery bank 300% to increase lifetime 400%), but less so for flashlights.
A lot of people take the shipping-recommendation as a storage-recommendation, and a lot of people take the quadrupling of cycles but miss the tripling of cycles needed.
The takeway key-points should IMHO be;
- Don't obsess over this. You could maybe have a small gain, but for most it's too much hassle to be worth the effort.
- Don't stress about fully discharging a battery, or charging it fully up. Charging a bit here and there is actually fine, and even good for the battery.
- There's no point (or gain) to having a routine of monthly "top ups" to stored batteries. (But there value in checking them periodically, like oeL mentions).
- If you want them fully charged for an emergency, go for it.
I'd rather store a battery with a bit too high a charge, than a bit too low. Personally I'm probably going with 70-80% somewhere, but wouldn't care too much if my charger didn't allow me to easily set a custom voltage to charge to.
edit to add; take the specific numbers with half a grain of salt, they're intended to illustrate the point, not be specific figured for any given cell.