One issue we're having at the moment is analysing traffic for various virtual hosts (in both Apache and Nginx). A combination of scripting and munin has proven OK, but not ideal. As we're on a cloud infrastructure, working out where traffic is coming from and what specifically is causing it is key.
Our alert and support processes are also currently being reworked; insight into server metrics is useful, and alerts based specifically on certain criteria is a must. Nagios has proven useful for alerts but the overheads in setting it up for each server/service is too much for our small team.
A dream scenario would be a dashboard of servers and services with a basic view of status (OK, warning, critical) that we can have in our office
The main problem we have is setting this infrastructure up; although most of this is achievable, we're looking for any SaaS that can provide this level of insight out of the box. Possibly a pipe-dream, but worth asking around!