Some comments on battery technology, as it relates to the "charge percentage".
Lithium-ion batteries have one feature, that the manufacturer should take care of: if you charge the battery fully (100% -- not according to the indicator, but in reality) while the battery is cool and then the battery is warmed up, it's charge increases (yes, over 100%) and that destroys the battery chemistry. The battery will be either immediately dead, or will hold much less charge. This is the reason why you are advised to never charge the battery while hot and never put your device in excessively hot place (like in a closed car under the sun).
Another issue with lithium-ion batteries is that they get damaged when deeply discharged, too. For this reason, any modern lithium-ion battery has internal electronics that will shut down the power when the battery goes below say 10% of charge.
Even if you do not use a lithium-ion battery, that is do nor charge/discharge it's chemistry slowly degrades. So there is absolutely no point in buying a spare battery and keeping it somewhere for a year or two. After that time, it will be almost as 'dead' as the one that you use. (ok, a little bit better, but definitely far from 'new')
This is the price we pay for light, high-capacity battery technology.
Lithium-ion however has one great benefit: while other battery technologies count each charging as separate cycle, with lithium-ion batteries the cycle is when you consume and fill up the battery's nominal capacity. Today's batteries survive 500-1000 cycles. Apple guarantees that your battery will hold 80% of it's capacity after 400 cycles. (which is one or two years according to the current iPhone 4S battery life)
From all this, it follows, that in order to provide greater life for your battery, Apple has to let you cycle only part of it's capacity. It is apparent, that when you charge the battery at "100%" it is not really charged that much. The typical charging technology for a lithium-ion battery is to charge the battery 'normally' up to 80-90% (I believe this is when your iPhone displays 100%) and then if you keep it plugged, continue to 'trickle charge' it further, at very slow pace. I believe it never charges more than 90-95% in order to provide for sudden warming of your phone when fully charged. Remember: less warming when the battery is 100% full == much longer battery lifetime.
There are lot's of 'battery utilities' in the App Store, that in my opinion do not do anything to improve your battery charge - the only provide more graphical indication of the process -- all charging is done by a charging circuit within your iPhone and that I believe is not programmable by any application, perhaps the only useful function is to notify you when your phone has finished 'trickle charging'.