<p>in XSLT processing, is there a performance difference between apply-template and call-template? In my stylesheets there are many instances where I can use either, which is the best choice?</p>

apply-template and call-template do not perform the same task, performance comparison is not really relevant here.
call-template takes a template name as a parameter whereas apply-template takes an xpath expression. Apply-template is therefore much more powerful since you do not really know which template will be executed.
You will get performance issues if you use complex xpath expressions. Avoid "//" in your xpath expressions since every node of your input document will be evaluated.