It may be time to resize the SaveFile if the indicator (bottom right-hand size of panel) has gone from green to amber, or even red.
Check that any temporary files are cleaned out, for example browser cache. #/root/# has various caches. There's one for openoffice, gnome-player, adobe, etc... (large directories like .mozilla folder, or files like libflashplayer can be symlinked out. If indicator went amber after installing Pet packages then it is best to expand the SaveFile.
Look the your /initrd/pup_rw folder to see what is in the save-file.

There is a tool for expand the SaveFile under - PuppyMenu > Utility > Resize personal Storage file
Or go to - PupControl > Drive > Resize Puppy File

Choose how much to expand the file, however it will only be activated on next startup. Ensure you restart with the file that needs to be expanded. This tool only allows you to expand the file, not decrease it.

SaveFile
How to avoid loading SaveFile
Pupsave Backup program
updated "resize pupsave" in Xdialog
Save file clarification