'S' is the number of lipo cells wired in series in a lipo battery - 3S is three lipo 3.7v nominal cells wired in series. Wiring in series causes the voltage to add and 3S = 3.7v x 3 = 11.1v nominal. There is another letter you sometimes see - 'P' is the number of cells wired in parallel. Like a 3S2P - that is done mainly to increase capacity, but it would be 3 cells wired in series and then another 3 cells wired in series, then these two groups of cells then wired together in parallel. It would have 6 total cells. Its not done much anymore cause lipos usually have plenty of capacity without adding the complexity.
Sizes are not standard at all, its an area you have to worry about - the lipo fitting where it needs to go.
Lipo is not like NiMh cells - they do not need to be discharged, doing so just basically wastes lipo cycle life. The only time a lipo should be discharged is to bring it to storage conditions. Say you charged one and then didn't use it and its going to be some time before you would use it, then you'd discharge it to ~3.8v/cell for storage. Leaving lipo sit fully charged is not the best for long life. There are storage modes on lipo capable chargers that handle this.
You can recharge them as many times a day as you want, there is no limit like NiMh. Maintenance is basically balance charging - balancing evens the voltage between cells. Storage charge if you're not going to be running it for week or more and if long term storage - recharge and discharge back to storage once a month (long term like all winter, several months).
Here's a decent intro -
http://www.rchelicopterfun.com/rc-lipo-batteries.html