After some long thoughts, I'm changing this rule for campaigns I run.  Favored Class is a pretty brutal penalty, and it is ridiculously easy to circumvent with racial HD, PrC's, etc.  While one level dips may be possible, I'm also going to handle that with a rule change.

So favored class rules are out.  Kaput.  I'm going to institue a 3 class rule, going forward.  Note:  This applies to main class only.  Gestalt is not included.

So for example:

Rogue [Warrior] 2/Swordsage [Warrior]6/Monk [Fighter] 9 will not incure penalties.

As a side note:  If a character does not show RP towards a second class, they will have a training period equal to 1 week per ECL to add that class.  This will only apply to radically different class types.  (Think "Barbarian" and "Cleric", or "Rogue" and "Warblade".  Fighter and Warblade would not incure this, up to DM discretion).

For example:  If a charater is playing a Fighter, and he wants to add a level of rogue at level 7, he either has to show his sneaky side (or attempts) during his 6th level, or else he has to spend 6 weeks training on rogue skills (think downtime) prior to adding that level.