As you are likely to know, every time you level someone up using Bonus Experience, three of their stats will increase. However, it is better to save your Bonus Exp for a character's later levels, when they have maxed out some of their stats. This way, when you use it on them, stats that they normally wouldn't gain much increases in will suddenly start skyrocketing.
For example, Micaiah is almost certainly going to max out her stats in Magic, Resistance and Luck (if Light Sage) very quickly, but lacks in some of the other stats, most significantly Speed, as she's usually too slow to double attack most enemies. However, when her Magic, Resistance and Luck are maxed out, start using Bonus Experience and watch her Speed rise.
Added by: Volke Dec 9th 2009, ID#3359