I use Nutrition Data. If you use their tracking tool, you will get very detailed vitamin, mineral, and fatty acid breakdowns, and you can get the information calculated for the entire meal or day rather than food by food. I find that inputting foods by gram or oz weight as opposed to their averaged sizes makes an enormous difference in accuracy, too.
Not quite as convenient as FitDay or the like, but it does give you a pretty exhaustive breakdown of everything from vitamins/minerals to fatty-acid composition. How accurate their breakdowns are is of course up for debate.
I use MyNetDiary. I really love it. It's quick to enter data. It has an iPhone app that syncs with the online database. Mobile food logging baby! It also keeps track of macronutrients and exports reports to Excel. However, it's not free.
Another one, that I don't see listed is www.sparkpeople.com . It probably isn't the right fit for your particular needs, but is a great site for someone who is completely clueless about nutrition and health... a good starting place, mostly because it eventually got me here ;-)