Edit xml using powershell

PowerShell is pretty flexible when working with [Xml] types. In the following example I'm reading in your xml from above (fixed some xml format errors), then using an array of hashes ($replacements) to specify which named dependent assemblies should have which newVersion values.

[Xml]$doc = @"
<configuration>
  <runtime>
    <assemblyBindings>
      <dependentAssembly>
        <assemblyIdentity name="A" publicKeyToken="5d861ad8ad8cd06f" culture="neutral" />
        <bindingRedirects oldVersion="0.0.0.0-68834.68834.68834.68834" newVersion="4.5.0.103" />
      </dependentAssembly>
      <dependentAssembly>
        <assemblyIdentity name="B" publicKeyToken="ae714df8cd90bc8f" culture="neutral" />
        <bindingRedirect oldVersion="0.0.0.0-65534.65534.65534.65534" newVersion="3.0.0.103" />
      </dependentAssembly>
      <dependentAssembly>
        <assemblyIdentity name="C" publicKeyToken="22955931b98512b6" culture="neutral" />
        <bindingRedirect oldVersion="0.0.0.0-65534.65534.65534.65534" newVersion="8.0.0.103" />
      </dependentAssembly>
      <dependentAssembly>
        <assemblyIdentity name="D" publicKeyToken="585a888b4a9ba2e3" culture="neutral" />
        <bindingRedirect oldVersion="0.0.0.0-65534.65534.65534.65534" newVersion="2.5.0.1286" />
      </dependentAssembly>
    </assemblyBindings>
  </runtime>
</configuration>
"@
$replacements =@(@{'name'='C'; 'newVersion'='0.0.1'},@{'name'='D'; 'newVersion'='0.0.3'})
foreach($replacement in $replacements)
{
  $doc.configuration.runtime.assemblyBindings.dependentAssembly | `
     Where-Object -FilterScript {$_.assemblyIdentity.name -eq $replacement.name} |% `
     {$_.bindingRedirect.newVersion = $replacement.newVersion}
}
#Output the raw xml to show the changes:
write-host $doc.OuterXml

The foreach is iterating through the elements in $replacements, and then finding the matching dependentAssembly by its assemblyIdentity.name, and then updating the newVersion value.