We had the same problem on tomcat, our problem was java options.
Unexcepted Garbage Collection caused server  slow down.
Java Options: min and max memory allocation settings.
The maximum memory should be up to 80% of your computers RAM. For example, if you have 512MB of RAM then you should set the maximum memory to around 400MB. To change the memory specifications you need to add this code to the Java Options text area:
-Xms100m -Xmx400
for 1g of RAM (server) and 1g of RAM (Mysql)

maxcount=150maxactive=400 mincount=100

max_connections in mysql=500 was a stable point.