Windows Task Manager should help. First, you'll need to bring out additional columns. Switch to the processes tab, then click view then columns. From here, choose at least the following:
Image name (the program's executable)
CPU (the amount of CPU usage)
Page fault delta (when this gets very high, CPU usage sky rockets)
I/O reads (the number of times the hard drive is being accessed for reading)
I/O writes (same as reads but for writing)
I/O other (not entirely certain on this one, probably memory)
Extra elements, if you have space, could include these:
Peak mem usage (the most memory a program has used since running)
Base Pri (the priority of the program for processing (most should be "normal"))
Handles (basically, pointers, a programming term)
Threads (separate routines of a program that runs separately)
I use these, and a few others, for my programming needs, so I can keep an eye out for hidden bugs in my programs and also optimize them (or terminate them if an infinite loop occurs). I've also used this to assist in bug hunts for other programs, such as Zonealarm and uploading causing increasing amounts of page faults and with it, CPU usage, eventually crashing my browser. Chances are, if something is amiss, there's a bug present. Identifying the program will help diagnose the problem.
Taking a screenshot of what you see when you're experiencing the slow down will be of great use.