Multiple instance in one server
The idea of having multiple instances on one server can have various reasons.

1. SQL Server License Costs

You can have multiple instances all running on one (big?) server and not have to pay large amounts of licensing fees.


  Disclaimer
  This depends on your licensing model, your license agreement and probably requires additional clearance by your certified reseller / licensor. Do not take this statement for granted. Your costs/licenses may vary. No guarantee given. 


2. Upgrades / Service Packs / Cummulative Updtes / Hotfixes

Having multiple instances on one (big?) server, allows you to patch the individual instances to different levels. You can have once instance running Service Pack 1 and another instance running Service Pack 2. And on another instance you could even test drive the hotfix you're not sure it will work well.

3. Permissions / SQL Server Roles / ....

Having multiple instances allows you to assign the sysadmin server role to individuals, without giving them the ability to destroy all the databases if they would be located on one instance. You have a separation between databases of one customer and another customer.

4. Windows Server Licenses

You can save on Windows Server licenses, because you only require one server license for multiple SQL Server instances.


  Disclaimer
  This depends on your licensing model, your license agreement and probably requires additional clearance by your certified reseller / licensor. Do not take this statement for granted. Your costs/licenses may vary. No guarantee given. 


5. Individual IP Addresses for Each SQL Server Instance

You can setup the individual SQL SErver instances to only respond to one IP address which in turn is linked to a CNAME/ALIAS. e.g. you could have your Windows Server running on 10.0.0.1 and each of your SQL Server instances running on 10.0.0.2 ... 10.0.0.5 which in turn would have their own CNAME:

10.0.0.1   hostname
10.0.0.2   hostanme-alias1
10.0.0.3   hostname-alias2


Each instance is then only reachable via the IP address and Port 1433 which in turn allows for IP to IP firewall configuration. 

See my question Configure SQL Server Analysis Services (SSAS) to run on same IP as SQL Server instance for an example of how you could configure multiple instances. Or the question Multi-instance SQL Server Standard Editon MaxDop settings where I show how we setup multiple insances at our shop.