If something "holds a special place" in your heart, it means that it's very emotionally important to you. For example:

Vikki will always hold a special place in my heart.

That job was horrible... but strangely enough, it still holds a special place in my heart.

You usually use this phrase to talk about things that you don't encounter very often any more, like a friend from your school days, a neighborhood that you don't live in any more, a pet you had when you were a child, etc.