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Sometimes charging Li-ion batteries is described as a very complex and difficult thing. Actually it is fairly simple: Charge with a constant current until the battery has reached its target voltage, then keep that voltage by reducing the charging current until the current reaches a threshold, then charging is finished. This method is called “CC/CV” (constant current, constant voltage) and there are charging controllers available implementing this very well for just a few cents (that is what you find in most flashlights).

The devil is in the details: Most importantly, don’t overshoot the target voltage by much (otherwise the battery might be damaged). Actually most chargers are able to achieve this quite good with a fixed voltage of 4.20 V (the normal target voltage of most Li-ion batteries).
Depending on the battery capacity and electrical characteristics, you want a different charging current. As a rule of thumb, small batteries are charged with a low current, large batteries with a high current. Some chargers allow you to choose between 2 to 4 different currents, often not low enough for very small batteries. Some chargers also come with an auto mode which automagically determines the best charging current (usually depending on the internal resistance of the battery).
Always charging a battery to its maximum capacity will shorten its lifetime. If you can spare 20% capacity, the lifetime will be increased dramatically. Nice, but most chargers won’t allow you to set a different target voltage. D’oh!

So while the actual charging process is fairly simple, you might want to have more control over the charging parameters. This is when you want a programmable charger like the S8000 or S4000 Pro.