It's hard to know what's not working on your page without more details.  Let me show you an example custom controller and a working page.  Put those in your org and see if the lookup works.  If it does, use these examples to make your own content work.

First, the controller

public class contactController {

// Return a list of the ten most recently modified contacts
public List<Contact> getContacts() {
return [SELECT Id, Name, Account.Name, Phone, Email
FROM Contact
ORDER BY LastModifiedDate DESC LIMIT 10];
}

// Get the 'id' query parameter from the URL of the page.
// If it's not specified, return an empty contact.
// Otherwise, issue a SOQL query to return the contact from the
// database.
public Contact getContact() {
Id id = System.currentPageReference().getParameters().get('id');
return id == null ? new Contact() : [SELECT Id, Name
FROM Contact
WHERE Id = :id];
}

}

Now the page

<apex:page controller="contactController">
<apex:form >
<apex:pageBlock title="My Content">
<apex:pageBlockSection title="My Content Section" columns="2">
<apex:pageBlockSectionItem>
<apex:outputLabel value="Lookup to an Account" for="theLookup"/>
<apex:inputField id="theLookup" value="{!contact.AccountId}"/>
</apex:pageBlockSectionItem>
</apex:pageBlockSection>
</apex:pageBlock>
</apex:form>
</apex:page>

While the controller will take a param, you don't need to specify it.  Just visit the page and you should see a single field with a lookup on it.