The desktop.ini is needed but only in the system32 folder. The thumbs.db is used for thumbnail creation of pictures in said folders. It's deletable but will recreate if a picture is put into the folder.
You might try the Folder options in Explorer. Under View, put a check in Hide extensions for known types.
Does looking at them hurt your eyes or something?
In many of my folders, there are files by the names "desktop.ini" and "Thumbs.db". Although I'm no windows-wiz, I reckon these files shouldn't be deleted. However, I would like them to be "invisible", so I don't constantly have to look at them. Is that possible?