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1. Java EE Examples : https://github.com/javaee-samples/javaee7-samples
2. Java Desing pattern with examples : https://github.com/iluwatar/java-design-patterns

Following open source projects I found well designed and well written in java

Netty - netty Elastic Search - elasticsearch Netflix Curator - curator Netflix Hystrix - Hystrix

GitRepo with Questions for projects : https://github.com/karan/Projects

For php, Rython and JS Projects : https://github.com/SambitAcharya/Mini-Projects