What are some good tools to use to manage high network traffic and the use of system resources?

I'm a long-time web developer but only have about a year's worth of experience messing around with Ubuntu (10.04 Server) on the command line. I've been playing with EC2 instances in the Amazon cloud, and though I have a pretty good grasp of of the EC2 and AWS concepts, I'm not really well versed in things like figuring out bottlenecks, creating and analyzing system logs, etc. What are some tools that you use?

Specifically, I am running on a LAMP stack (apache2). MySQL is running on a separate, dedicated instance. The plan is to eventually get everything on a load balancer and add/remove instances as needed.