Agreed, the self protection built into newer batteries should prevent the cell becoming completely discharged and thus unable to be recharged. But it is generally stated as good practise to not run them down completely; and it is definitely not necessary.
As far as the "mythical 16 hour charge" goes, there have been several discussions. My view on the matter after playing around with Lithium technology batteries is the following:
The 16 hour charge is not necessary in that the battery must be held charged for 16 hours, as was the case with Nickel technology batteries. However, it can be useful. As the battery charges for the first few times its resistance is slightly lower, and the battery can "peak" slightly too early. At this point, the charger will switch off. During the next few minutes the battery will discharge to maybe around 90-95%. As soon as it does, the charger will kick in again until the battery reaches 100%. This will continue until the battery really does reach 100% charge. This is when the charger can be removed.
Making sure it reaches 100% for the first few charges is important in that it calibrates the internal battery meter. For the same reason, on the first 2-3 charges it is worth running the battery down to about 10%. After this, however, that is no longer required or recommended.
So whilst the full 16 hours is not required, it won't hurt, and it will ensure the battery is fully charged. Having said that, once the phone says it is fully charged, leaving it on charge for another, say, two hours will do the same job. In effect, it is a matter of giving the battery enough time to set itself up, and not switch of the power as soon as the phone says "charged" for the first time.
Jon