Pop-ups are great to boost sign ups (newsletters, accounts, etc.). But you can use them to promote more strategic content, such as :
- Coupons & offers
- Social & Fanpages : Facebook, Twitter, etc
- Breaking news
- Content to download : Whitepapers, mobile app, etc.
- Customer service
- A welcome message, or any other message for your visitors
In all those cases you will give this content a great impact, and you will improve conversions the same way than you boost sign-ups.