Actually, discharging your battery doesn't necessarily help your battery life. Batteries are rated for x (usually 500 or so) discharge/recharge cycles before they suffer large performance decreases.
If you really want to extend the life of your battery you should take it out when you're plugged into the wall. Heat is what really kills battery life.
It's also worth noting that leaving your battery in while connected to the wall doesn't over-charge and harm your battery. Your computer/battery has built-in safeties that prevent that from happening, so when you're on wall power the batter is only being charged when it's below its maximum charge. But like I said above, if you really want to increase battery life you should take the battery out while on wall power as heat is a big toll on batteries.
I think you were misunderstanding what what happening with the Fn+F3 combination. I've never heard of a battery discharging while the power was plugged in - unless the power cable was broken of course. The cable provides enough juice to both power the laptop and charge the battery at the same time. If you're plugged into the wall, you're only using wall power, not battery power to use your machine - so when it's plugged in no battery power is being used, how could it discharge?
If I'm not mistaken (and I very well may be - I haven't used Windows since 2007) Fn+F3 does different power modes in Windows. There's Performance mode, Power Save, and Balanced. I believe Fn+F3 cycles between these profiles in Windows, but when you're plugged in they don't make a difference. The only thing close to this in Ubuntu is CPU frequency scaling which is set to a governor of ON_DEMAND be default, meaning your computer runs at the lowest frequency (My Inspiron 1525 w/ 2.4Ghz Core2 Duo is 800Mhz lowest freqency) until more power is needed for a task. This helps with head and overall wall power usage when plugged in. It is possible, however to override it to use the POWERSAVE or PERFORMACE governors using the
cpufreq-set command like so:
cpufreq-set -c 0 -g performance (replacing -c 0 with -c 1, -c 2, etc for all your cores). That will set your computer to use its max frequency all the time.