can someone please help

bought a new harddisk of 120G vs old one of 20G, and reinstalled w2k system, the speed is slower than ever, i last checked there were 700 thousands files on it(i put all research papers, softwares, references cumulated over last 5 years or so on it). without vires, is it normal? do not buy a new computer, any idea how to improve the performance, i am not a guru, but an ok player with computers. any suggestions will be appreciated.