I can think of at least a couple based upon:
• Leveling up
• Affection (usually happiness. Maybe even hate, correct me on this)
• Day and Night cycle
• Trade (like Kadabra and Machoke)
• Trade with an Item (like Scyther)
There's got to be some others for sure, after all I didn't play gen 4 and it's not like I have completed a Pokédex since R/B/Y, so I must have missed a few.
Help me out here guys!