We all are seeing that Salesforce1 is evolving with every passing day and there is yet lot to be done. One of the many items is a custom lookup field on a Visualforce page.
Lightning design systems do provide us with the CSS we can use to create lookup fields the logic has to be written by the developer. Below is a basic example that can be used to implement the basic autocomplete version of the lookup field.
The auto complete text box is implemented using the CSS provided by Salesforce1 lightning design.
The Visualforce page uses Visualforce remoting to fetch records based on the user input. A call to the controller method is made every time a keyup event is fired and the results are updated.