Based on the data you get from the cmdlet get-agent you can list all agents with a specific setting.

This line for example, will list all agents with the Agent Proxy setting enabled:
get-agent | where {$.ProxyingEnabled -like $true}_

Change $.ProxyingEnabled_ to $.ManuallyInstalled_ and you’ll get a list with all manually installed agents.

In OM2007 SP1 there is a bug on updating the ManuallyInstalled property, so that wont work. This is corrected in R2.
If you dont have to use powershell there is a workaround in this thread.

 
Your options are:
PrimaryManagementServerName
Id
LastModified
Name
DisplayName
HostComputer
HostedHealthService
HealthState
PrincipalName
NetworkName
ComputerName
Domain
IPAddress
Version
RequestCompression
CommunicationPort
MaximumSizeOfAllTransferredFilesBytes
MaximumQueueSizeBytes
ManuallyInstalled
InstallTime
InstalledBy
CreateListener
AuthenticationName
ActionAccountIdentity
HeartbeatInterval
ProxyingEnabled
ManagementGroup
ManagementGroupId