Getting metrics from logs and various other sources into Graphite is quite simple. The most interesting metrics do represent critical performance data, and the pro-active-monitoring approach, means a person sitting there and waching the dashboard, isn't suited to our needs. We use Nagios with Centreon as our monitoring plattform, and we want to alert on some of the metrics collected in Graphite.
My current project is to take our Weblogic monitoring setup from parsing gc logs in Splunk up to the next level. For other things metrics we do use Graphite already. Graphite is an awesome app for graphing any sort of metrics. You just need to get them in there somehow. Some days ago I stumbled over an outstanding piece of software written by Dimo Velev: metrics-sampler.
Update 2013/10: we decided to replace Graylog2 with Kibana3 completely. The article below is just for reference, the logstash config is outdated since logstash 1.2 and the setup as described below is suboptimal anyway. I'll post a new article shortly.
Update 2014/02: Finally, the new guide is here: Indexing and searching Weblogic logs using Logstash, Elasticsearch and Kibana.