I was struggling to find the specific types of warnings to suppress. So here is a list of Warnings that can be suppressed:

Unused code:

• UnusedPrivateField
• UnusedLocalVariable
• UnusedPrivateMethod
• UnusedFormalParameter

Naming:

• ShortVariable
• LongVariable
• ShortMethodName
• ConstructorWithNameAsEnclosingClass
• ConstantNamingConventions
• BooleanGetMethodName
• VariableNamingConventions
• MethodNamingConventions
• ClassNamingConventions
• AbstractNaming
• AvoidFieldNameMatchingTypeName
• AvoidFieldNameMatchingMethodName
• NoPackage
• MisleadingVariableName

Design:

• ExitExpression
• EvalExpression
• GotoStatement
• NumberOfChildren
• DepthOfInheritance
• CouplingBetweenObjects
• DevelopmentCodeFragment

Controversial:

• Superglobals
• CamelCaseClassName
• CamelCasePropertyName
• CamelCaseMethodName
• CamelCaseParameterName
• CamelCaseVariableName

Code size:

• CyclomaticComplexity
• NPathComplexity
• ExcessiveMethodLength
• ExcessiveClassLength
• ExcessiveParameterList
• ExcessivePublicCount
• TooManyFields
• NcssMethodCount
• NcssTypeCount
• NcssConstructorCount
• TooManyMethods
• TooManyPublicMethods
• ExcessiveClassComplexity

Clean code:

• BooleanArgumentFlag
• ElseExpression
• StaticAccess
• BooleanGetMethodName
• ConstantNamingConventions
• ConstructorWithNameAsEnclosingClass
• CouplingBetweenObjects
• CyclomaticComplexity
• DepthOfInheritance
• EvalExpression
• ExcessiveClassComplexity
• ExcessiveClassLength
• ExcessiveMethodLength
• ExcessiveParameterList
• ExcessivePublicCount
• GotoStatement
• LongVariable
• NPathComplexity
• NumberOfChildren
• ShortMethodName
• ShortVariable
• TooManyFields
• TooManyMethods
• UnusedLocalVariable
• UnusedPrivateMethod

Here are some NCSS related (not sure if they work), for by the time of this writing they were commented:

• NcssMethodCount
• NcssTypeCount
• NcssConstructorCount

Example:

<?php

namespace Acme;

/**
 * @SuppressWarnings(PHPMD)
 */
Class UnavoidableComplication
{
}
?>

<?php

namespace Acme;

Class User
{
    /**
     * @SuppressWarnings(PHPMD.BooleanGetMethodName)
     * @return bool
     */
    public function getActive()
    {
        return $this->active;
    }
}
?>

The rules were extracted from these files.