Hi,
PennController provides a Template command that can generate trials from a CSV table, and CSV tables can optionally contain a Group (alternatively called List) column that further distinguishes subsets of rows, so that each time the experiment is run only rows from one subset are used.
You can find an example and discussion of it on this page of the documentation tutorial, which illustrates 4 items each associated with two conditions (Ending: -s vs Ending: No-s) but presented in only one condition to each participation (latin-square design). Take a look at the Table section of the page more particularly.
Let me know if you have more questions
Jeremy