Given your question is rather vague... here's my best answer:

1. You need to find a way to connect to Core Service from Java. Either generate a proxy from the wsdl as documented here or use a pre-built one from the community
2. Ask Tridion for a list of publications using the Core Service API, using something similar to this
3. Ask additional questions based on where you get stuck.

Given your question is rather vague... here's my best answer:

1. You need to find a way to connect to Core Service from Java. Either generate a proxy from the wsdl as documented here or use a pre-built one from the community
2. Ask Tridion for a list of publications using the Core Service API, using something similar to this
3. Ask additional questions based on where you get stuck.