Graylog2 is, in my opinion, a wonderful tools for collecting and searching your logs. The only problem I've had so far was updating it in CentOS, which my server is using as OS.
Here's a quick guide on how to succeed.
Step 1 - Read the graylog2 blog
Read this blog post and follow it when it comes to upgrading Elasticsearch. Elasticsearch 1.3.4 can be found here.
I also had to check the permissions for /var/log/elasticsearch and /var/lib/elasticsearch, they were owned by the wrong user and group.
Step 2 - Upgrade Graylog2
I did this by removing the old graylog2-packages, updating the repo from 0.90 to 0.91 and finally reinstall graylog2-server and graylog2-web. Download the latest graylog2 repo from here.
Now, your configuration files will be called graylog2.conf.rpmsave, restore the old config files for both graylog2-server and graylog2-web.
Start graylog2-server and graylog2-web again.
Done.