Keep clearing out what is generated by your programs as described back in Removing the Junk. Just because you took it out once doesn't mean any of it stays gone.

If you ever reinstall Windows obviously you will have to do as described in Cleaning out Windows, but even if you just do a system restore using the CD, it also applies. Revisiting this every so often won't hurt, especially as new discoveries of junk are made and added.

Defragment the hard drives. This should be done at least monthly, more if you surf the internet, send and receive email, or install and uninstall software a lot. Windows own defragmenter works decently, but for FAT 32 drives (used by Windows 9x family) Norton SpeedDisk is a very good program. Other defragmenting programs are out there, but always do your research. Also remember: clean first, defragment second.

Edit your bootup functions. If you did not already, you should set the drive parameters in the BIOS instead of detecting them automatically each time you start up. Both in Windows and in the BIOS there are settings that search for floppy drives when you start up. Most people will not be adding such drives frequently, and if you do add a floppy drive you can set them up manually as you need to. In the BIOS you disable "bootup floppy seek" and "floppy drive swap". In some Windows 9x versions right click My Computer and choose Properties then go to the Performance tab, then the File System button. Under the Floppy Disk tab, Settings section, uncheck "Search for new floppy disk drives each time your computer starts" the click Apply, then OK.

Clean and compress the registry. This is a task best left to programs meant to do it automatically. Mistakes made when editing the registry can lead to Starting Over. Microsoft's own RegClean is a good application for fixing key portions of the registry, especially when cleaning the registry immediately following a fresh install of Windows. Norton Windoctor is a good application as well, and there are others (even free). I sound like a broken record, but research... You can compress the registry by hand by booting to MS DOS mode and giving the commands:

regedit /e all.reg

regedit /c all.reg

This creates a .reg file that is a copy of the entire registry and then imports it back compressed. The nice feature of this method is you now have a full backup of the registry. Occasionally Windows chokes, won't quite import the compressed registry, and goes back to the old one before you started. If it doesn't go back, just run the file you made and you are good. Again there are programs to do it, as included in Norton Optimization Wizard. These tasks are especially important when you install and uninstall a lot of software, as they leave 'orphans' that bloat your registry.

Clean out old .chk files. These are created in FAT 32 file system volumes when you do a hard (crash) shutdown in the root ( C:\ ) directory. Any file not fully written back will be left in unallocated fragments. Most often these are just temporary files and hence disposable. By opening an MS DOS prompt and using the type command to view the content of these files, you can determine in most cases if they are just temporary junk. If your system has run fine without them for a while anyway, chances are it will continue to do so. Delete em.

There are a few others fine tuning items you can use. For the Windows 9x family here are some items that give you abilities already found in some degree in the Windows NT family. One is a program that scans for unused .dll files that are left when you uninstall programs or when Windows has installed them in anticipation of you needing them. You can find this program Clean System Directory at http://www.theabsolute.net/sware/#clnsys (not for use with any NT based OS or ME). This is a great program and has a backup feature. There are more out there as well. For finding programs running in the background in Windows 9x that you can't see in the Close Program dialog (unnecessary driver helpers, utilities that hide as services at startup, and even trojans and virii) there are 2 programs recommended, Memload and TaskInfo. Memload just shows you what is there, Taskinfo can directly interact with them - which can be treacherous. Be careful about what you try to shut down. Research... You can see all processes in the Windows NT family via Task Manager, so the extra utilities are not needed for them.