Is there a way to write a custom apple script or any other way to get a Alert or Desktop notification when the battery on my Macbook Pro reaches a certain percentage of charge?
This app is a free replacement for the standard battery menu bar item, and it includes the ability to set notifications (in Notification Center) when the battery hits certain percentages.
Alternatively, if you want to rig your own solution, you can get charging status and percentage from running
pmset -g batt in the shell. You'd need to poll it rather than getting notified however. If you're comfortable with programming, the IOPowerSources API looks like it can do notifications when the battery/charging status changes, but obviously that's more involved.