For now, stick to reporting them in chatin chat or here on MSO. Don't flag the user's other SO questions. (We are looking into getting a basic flagging system up on Apptivate. Watch this space for the decision.)
Update:
This has been implemented. Users with at least 15 rep on Stack Overflow will see a "report this app" link below the left sidebar on every app page. Apps that are spam, dupes, or otherwise need staff attention should be flagged using this link.