[SalesForce] Generating package.xml for deploying with Ant from Eclipse

First, you need to ensure your package.xml contains at least what you are deploying. It may contain more, but not less.

<types>
    <members>Class1</members>
    <members>Class2</members>
    <members>Class3</members>
    <name>ApexClass</name>
</types>

UPDATE: It is even easier to do this:

<types>
    <members>*</members>
    <name>ApexClass</name>
</types>

Next, setup an ant target in your build.xml which looks something like this:

<target name="QADeployClass1And2">
    <delete file="deploy.zip"/>
    <zip destfile="deploy.zip">
        <fileset dir="src" includes="classes/Class1.*"/>
        <fileset dir="src" includes="classes/Class2.*"/>
        <fileset dir="src" includes="package.xml"/>
    </zip>
    <sf:deploy zipFile="deploy.zip" allowMissingFiles="true"
        username="user@org.com.qa" password="**********" 
        serverurl="https://test.salesforce.com"/>
    <delete file="deploy.zip"/>
</target>

When you run this target you will deploy only Class1.cls and Class2.cls. I also find it useful to place the username, password and serverurl on the target so that I can use a different ant target for each target org without having to switch out the build.properties file.

I use the zipfile approach (1) because this allows me to easily and centrally control which files go into the payload. If you wish to use a folder with deployRoot you need to make a temporary folder and copy in the files you need:

<target name="deploy1">
    <delete>
        <fileset dir=".\deploy\classes" includes="**/*.*"/>
    </delete>
    <copy file="deploy\package1.xml" tofile="deploy\package.xml"/>
    <copy todir=".\deploy\classes">
        <fileset dir=".\src\classes\" includes="Class1.*"/>
        <fileset dir=".\src\classes\" includes="Class2.*"/>
    </copy>
    <sf:deploy allowMissingFiles="true" username="${sf.username}" password="${sf.password}" serverurl="${sf.serverurl}" deployRoot="deploy"/>
</target>

In this example you could setup package1.xml to only include the files you want to deploy and it will overwrite package.xml when you run this ant target thus making allowMissingFiles="true" superfluous.

One possible solution is to use Packages as a container for your code. This allows you to retrieve only the code in your package from an org which ignores all other metadata in the org such as managed package fields, standard Salesforce fields, and any customer created fields.

To test it out, go to Setup->Create->Packages in your source org. Create an unmanaged package and use the Add Components button to add all the metadata you want to bundle in your package. Then, retrieve all metadata from the package into a folder. You'll wind up with a folder containing all the metadata and a package.xml file formatted to allow deployment into a Package in your target orgs.

The key difference in the package.xml is the inclusion of the element which flips on the deploy to package functionality.

The one catch is the target org will need to have a package with the same name already created before the deployment but this is a one time manual step per target org.

I just wrote up the build.xml targets in a different answer you can reference here: https://salesforce.stackexchange.com/a/31437/4832

There are, however, some drawbacks. Some metadata types won't deploy this way. For example, ActionOverrides don't work this way as they can't be bundled in a package. As a workaround, you can create a normal bundle of metadata for use only in deploying the types you can't deploy as part of a package.