How can I "clip" shapefiles to a box-shaped subset without using the ESRI ArcMap tool?

Our marine data training program (www.oceanteacher.org) tries to avoid necessary use of commercial software, and so far we've been able to stay nearly ESRI-free.  But the one Arc tool that we still find necessary is the clip function that cuts a shapefile down to the borders defined by a second shapefile.  In our case, the second shapefile is almost always a simple rectangular box (area of interest).

Does anybody know a free, stand-alone program (hopefully a binary executable) that can do this also?

Thanks in advance for any help.

Murray Brown
UNESCO-IOC Marine Data Mgt. Training Program

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