Here are some online certificate course for Computer Science Engineering.
1. Oracle DB Certification
2. Oracle Java Certification
3. Microsoft Certification
4. Cisco Networking Certification
5. Red Hat Linux Certification

Some of the good certification courses for computer science engineer are:

For software testers: ISTQB certification

For Java developers: Sun Microsystem certification

For Database developers: Oracle certification

For .Net Developers: Microsoft certification

For networking engineers: CCNA and CCNP certification

Hope this helps you!