I had the same question last week and tried several options.
For basic snmp graphing needs, cacti is great, but graphing apache, mysql, etc. is a bit too hard I think.
ntop is also a nice tool, but has a different usecase than the other ones in your list.
You should look at Zenoss. The Core version is FOSS, userfriendly, and very powerful. I had no need for the Enterprise version, but your needs may differ.
It does graphing, monitoring and alerting of all the basic stats, but download some ZenPacks and you can easily add Apache, MySQL or many other stats. All configuration can be done via the GUI. The interface is clear and responsive and allows for easy management of very large networks.
In short, I'm glad I never spent much time on Nagios, because I believe Zenoss is the best option available.