Java/JAXB: Unmarshall XML attributes to specific Java object attributes

How about?

Introduce a common super class called Options:

import javax.xml.bind.annotation.XmlAttribute;

public abstract class Options {

    private String name;

    @XmlAttribute
    public String getName() {
        return name;
    }

    public void setName(String name) {
        this.name = name;
    }

}

Then on your class with the list of options (Configuration in this example), specify an @XmlJavaTypeAdapter on that property:

import java.util.ArrayList;
import java.util.List;

import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;

@XmlRootElement
public class Configuration {

    private List<Options> section = new ArrayList<Options>();

    @XmlJavaTypeAdapter(OptionsAdapter.class)
    public List<Options> getSection() {
        return section;
    }

    public void setSection(List<Options> section) {
        this.section = section;
    }

}

The XmlAdapter will look something like this:

import javax.xml.bind.annotation.adapters.XmlAdapter;

public class OptionsAdapter extends XmlAdapter<AdaptedOptions, Options> {

    @Override
    public Options unmarshal(AdaptedOptions v) throws Exception {
        if("default_options".equals(v.name)) {
            DefaultOptions options = new DefaultOptions();
            options.setName(v.getName());
            options.setDefaultPort(Integer.valueOf(v.map.get("default_port")));
            options.setLogLevel(v.map.get("log_level"));
            return options;
        } else {
            CustomOptions options = new CustomOptions();
            options.setName(v.getName());
            options.setCompatibility(v.map.get("compatibility"));
            options.setMemory(v.map.get("memory"));
            return options;
        }
    }

    @Override
    public AdaptedOptions marshal(Options v) throws Exception {
        AdaptedOptions adaptedOptions = new AdaptedOptions();
        adaptedOptions.setName(v.getName());
        if(DefaultOptions.class == v.getClass()) {
            DefaultOptions options = (DefaultOptions) v;
            adaptedOptions.map.put("default_port", String.valueOf(options.getDefaultPort()));
            adaptedOptions.map.put("log_level", options.getLogLevel());
        } else {
            CustomOptions options = (CustomOptions) v;
            adaptedOptions.map.put("compatibility", options.getCompatibility());
            adaptedOptions.map.put("memory", options.getMemory());
        }
        return adaptedOptions;
    }

}

AdaptedOptions looks like:

import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;

import javax.xml.bind.Marshaller;
import javax.xml.bind.Unmarshaller;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlValue;

public class AdaptedOptions extends Options {

    @XmlAttribute String name;
    @XmlElement List<Value> value = new ArrayList<Value>();
    Map<String, String> map = new HashMap<String, String>();

    public void beforeMarshal(Marshaller marshaller) {
        for(Entry<String, String> entry : map.entrySet()) {
            Value aValue = new Value();
            aValue.name = entry.getKey();
            aValue.value = entry.getValue();
            value.add(aValue);
        }
    }

    public void afterUnmarshal(Unmarshaller unmarshaller, Object parent) {
        for(Value aValue : value) {
            map.put(aValue.name, aValue.value);
        }
    }

    private static class Value {
        @XmlAttribute String name;
        @XmlValue String value;
    }

}