You can check the transparency of different elements, such as the fill or stroke, the blend modes, ... For the whole list of options, check the attributes of the Action in PitStop.
Transparency can cause some problems if you view documents in Adobe Acrobat 4.0 or earlier: transparent objects can be rendered incorrectly.
A transparent layer can also cause problems when you transpose the PostScript code of your PDF document to the halftone information of your printer (the 'ripping').
A typical example is saving graphics with transparent elements as PDF compatible with Acrobat 5.0 in Adobe Illustrator 9.0 or Adobe InDesign 2.0. In Adobe Acrobat 4.0, transparent objects in your PDF document are displayed and printed opaque, but transparency is not removed. If you open the same PDF document in Adobe Acrobat 5.x, the transparent objects will look (and print) fine again.
It can be useful to make the distinction between spot colors and CMYK colors when checking the transparency settings in your documents, because different rules govern the overprinting of spot colors.