1) Play the darn thing while giving myself time to 'smell the flowers' (i.e., for SHIII that means just dropping down to 1xTC and watching the waves every once in a while, or taking a tour through the interior with the free camera, to study rivets :p)
2) Listen to music (normally the grammophone packs + classical + Das Boot soundtrack)
3) Take down notes in my ever-growing collection of logs. A notepad is always on my desk and gets filled with notes even when I'm not actually making a coherent career log.
4) Stare at the charts and U-boat schemes I have all over my walls! When that fails, I go through the small atlas I have on my desk.
5) Talk to my brother if he comes in, or have occasional conversations with friends on IM (Alt+Tab is my friend!)
6) Check the forums! (I said Alt+Tab is my friend...)
7) In the more extreme cases, exercise (a few push-ups or curls never hurt anyone... I think), or cook (sometimes results in burned pottery, especially if I suddenly get detected and have to evade some depth charges...)