For those of you that are not familiar with the Property Bag concept, it is a place to store metadata or properties for your SharePoint objects. However, when exploring the SharePoint object model, I have noticed that SPWeb provides a Property bag to store metadata info related to a web site, where SPSite doesn’t. So the only way to store metadata info related to a site collection (SPSite) is to use the property bag of the root web.

SPSite  Represents a collection of sites on a virtual server, including a top-level site and all its subsites.
SPWeb Represents a Windows SharePoint Services Web site.

To store a property in the bag :

SPPropertyBag Bag =  site.RootWeb.Properties;
if (!Bag.ContainsKey("PropertyName"))
{            
      Bag.Add("PropertyName", "PropertyValue");
      Bag.Update();
}

And to remove a property, use the following snippet :

SPPropertyBag Bag =  site.RootWeb.Properties;
if (Bag.ContainsKey("PropertyName"))
{
    Bag["PropertyName"]=null;                            
    Bag.Update();
}

For more SharePoint code snippets, I would recommend SPCodeSnippets available at codeplex.