Solved: For when simple profiling isn't effective enough, I have written a tool to show me where performance hits occur. Basic information about how the tool works is in the accepted answer below. The source can be found here: http://pastebin.com/ETiW8hE8 (be sure to turn debugging symbols on in the program you're testing)
I've built a game engine in C++ and I have noticed in one particular area of a level that there is a brief performance hit. The game will stop completely for about half a second, and then continue on merrily. I've tried to profile this, but it's difficult isolate the condition since I also have to load the map and perform the in-game task which causes the performance hit. I can make a map load automatically and skip showing menus, etc, and comparing those profile results against a set of similar control data (all the same steps but without actually initiating the performance hit), but it doesn't show anything obvious.
I'm using gmon to profile.
This is a large application with many, many classes and functions. The performance hit only happens once, so there's no way to just trigger the problem many times during one execution to saturate my profiling results in order to make the offending functions more obvious in the profiling results.
What else can I do?