[SalesForce] Set Standard Objects as Menu Item in Salesforce1

Pinned objects are only part of the list of Smart Scope objects. Any other objects that the user has been interacting with over a period of time (including page views and clicks on search results) are automatically added to the Smart Scope, in addition to any pinned objects.

For the user where only the pinned objects are showing up, if they are a new user or don't have a lot of other activity in the system on other objects, that might be why no other objects are showing up.

Peter is totally right, the concept of and "App" in S1 is a little different. Also, I would like to add a little bit more about a new metadata type that S1 introduced in this release ( I think Peter know about it too and he also recommended to me a good way to explain it :) ) , that we could consider the new view of "Apps".

If we make ourselves the question, what is having/ containing the App that we know at this moment? What we know, an app can contain different tabs , that are pointing to different objects for example ( and sometimes tab related with VF pages), and what has a tab when you click on it? a default list view. Then we could say that an App contain a list of tabs with default list views.

Well the new metadata type that S1 introduced is "Flexipage" , the flexipage will allow us to have diferent list views in only one page and also ( that the really nice part) have quick actions on it. Then this Flexipage , will be like a container where we will be able to put different list views, filtered list views or related to recent records, and quick global actions.

The Flexipage will appear like another tab in that picture and you can put it down or up ( using mobile administration).

To finish , I need to say that this metadata does not have a UI creation in this version of Salesforce, the new metadata is only possible to be create by deploying it into the org ( using ant commands or eclipse...) Once the Flexipage is deployed into the org you will be able to find it in : Create -- > tabs --> Flexipage Tab , and you will be able to configure the icon too.

I leave you here a code example of flexipage :

<?xml version="1.0" encoding="UTF-8"?>
 <FlexiPage xmlns="http://soap.sforce.com/2006/04/metadata">
    <flexiPageRegions>
        <componentInstances>
            <componentInstanceProperties>
                <name>entityName</name>
                <value>Account</value>
            </componentInstanceProperties>
            <componentInstanceProperties>
                <name>filterName</name>
                <value>MyAccounts</value>
            </componentInstanceProperties>
            <componentName>flexipage:filterListCard</componentName>
        </componentInstances>
        <componentInstances>
            <componentInstanceProperties>
                <name>entityName</name>
                <value>Contact</value>
            </componentInstanceProperties>
            <componentInstanceProperties>
                <name>filterName</name>
                <value>MyContacts</value>
            </componentInstanceProperties>
            <componentName>flexipage:filterListCard</componentName>
        </componentInstances>
        <componentInstances>
            <componentInstanceProperties>
                <name>entityNames</name>
                <value>MyCustomObject__c</value>
            </componentInstanceProperties>
            <componentName>flexipage:recentItems</componentName>
        </componentInstances>
        <name>main</name>
    </flexiPageRegions>
    <masterLabel>My new App</masterLabel>
    <quickActionList>
        <quickActionListItems>
            <quickActionName>flexiAction</quickActionName>
        </quickActionListItems>
    </quickActionList>
</FlexiPage>

I hope it is helpfull :)