When you link up to pokemon sapphire on GBA, when your berry program updates..

It extends the lifespan of the time cycle in your game, and is a remedy for the 'berry glitch.'

I remember doing this after going through that glitch last week.

In your Sappire after a year of gameplay all time based events will freeze, like the rooftop sale in Lilycove's Department.

But you can fix that by hooking up to Colosseum.

In pokemon ruby/saphire after a long time, all time related events (like berries and special sales) will stop working. The berry program lets your berries grow again and all time related events start happening becuase it fixes the glitch.