I agree with Floyd, I like FT.com the best for tracking stocks. Its free and provides a wealth of information about your stocks and their performance over different time periods.
I also like that the FT.com Portfolio provides you with a summary of your portfolios. The other sites such as MSN and Morningstar only allow you view each portfolio separately.
Unfortunately, I also agree with Floyd that FT.com updates the mutual funds very late. Right now its 7:20pm pacific time and the FT.com Portfolio is reporting today's results for stocks and yesterdays results for mutual funds. The FT.com total porfolio value change for the day is incorrect. Rather than give you a total portfolio value change for the day, it gives you a blend of todays value change for stocks and yesterday's value change for mutual funds. Which is not helpful.