I am sure that there are plenty of differences between Windows 98 and 95. What is mentioned here (in passing) focuses on the things that really strike me as new and different from a system maintenance perspective.

MSConfig (System Configuation Utility) picks up where Sysedit left off. It puts a nice GUI around Windows features that were only accessible from obscure keyboard commands or the command line. For example, you can set the boot options from MSConfig instead of pressing F8 or F5.

WinAlign is not what ships with Windows 98. The program file WALIGN.EXE does. This file is run by the Task Scheduler by default. More details about this program (like what it does) is at:

http://www.winmag.com/windows/win98/alignfaq.htm

The Task Scheduler also runs a task called "Windows Critical Update Notification" by the hour. Yes, hourly! At some point this package was set to run every five minutes! For more information please start with:

http://www.aztcs.org/sigs/wintips9906.html