I save once I'm out of harbor in order to run SH3Gen. Then I'll save again if it's getting really late and I need to sleep. Twice I've saved right before a big expected battle, but once I realized that reloading that would erase any progress I'd done AFTER that I usually just forget about the saves and go on with whatever results I'd had.
Haven't even considered reloading due to a missed torp, only restarted due to time compression deaths since well, that's lame.