the default is the first one in the list of workitem types for this project.  so you can change the list.

you currently cannot limit the types displayed in the select workitem list.

This looks like an enhancement to me. 

The default can be changed for the pop-up which shows up from the Links Tab by modifying the configuration source which is not recommended though.

From your project opened in Eclipse Client > Configuration Source Tab > you will notices the list of work item types under the tag :

<data>
            <configuration-data final="false" id="com.ibm.team.workitem.configuration.workItemTypes" xmlns="http://com.ibm.team.workitem/workitemTypes">

Pick the <Type> ... </Type> you want to appear as a default and move it to the top and save it.

Some sample source which makes the story as a default is below:

<data>
            <configuration-data final="false" id="com.ibm.team.workitem.configuration.workItemTypes" xmlns="http://com.ibm.team.workitem/workitemTypes">
                <type category="com.ibm.team.workitem.workItemType.story" icon="processattachment:/workitemtype/story.gif" id="com.ibm.team.apt.workItemType.story" name="Story">
                    <alias name="user story"/>
                </type>
                <type category="com.ibm.team.workitem.workItemType" icon="processattachment:/workitemtype/bug.gif" id="defect" name="Defect">
                    <alias name="bug"/>
                </type>
                <type category="com.ibm.team.workitem.workItemType.task" icon="processattachment:/workitemtype/task.gif" id="task" name="Task">
                    <alias name="work item"/>
                    <alias name="workitem"/>
                    <alias name="item"/>
                </type>

Now on, when you get a pop-up for the work item type from the links tab, you will notice at the bottom that there is quick link to create a work item of type you moved to the top in the configuration source.

However, this does not affect the popup from the Work Item attribute in the work item. So, I see no other OOTB feature at the moment to get to this default.  Suggest raising an enhancement.

Hope this helps.