Junk files in music folders

I namually manage all my music folders, with each album being a subfolder of the artist folder. I do my best to keep junk files out of these folders when I edit the ID3 tags using Mp3tag or Tagscanner. Now that I've been using a program called Xinorbis to evaluate the contents of my music folders, I see that I have many junk files that don't show up when I simply open the folder. I believe I have "show hidden files" checked, but there are still some rogue files. Most of them are either .ini or .jpg (small album art stuff) with a few .db and .nfo files.
Does iTunes use any of these files? Any danger of deleting them? Will they be regenerated by iTunes or any other program? These files don't take up much space, but it does confuse things when "properties" shows several hundred (or thousand) files more than my mp3 count. (Mp3 13934 files, 3573 graphics files, 413 system files)
This is the first step of cleaning out the files so that I may run the script that will extract album art into the folders. You know, get rid of the old stuff first.

Adding to Katrina's answer slightly...
Windows Media Player & Windows Explorer may typically create up to 6 additional files in each album folder containing .mp3 or .wma files - sometimes more if you've tried getting it to refetch album information, for example because the first attempt gave the tracks in a different order. These are:
desktop.ini - records WMP's identification of the album
Folder.jpg - 200x200px album art, displays as a folder thumbnail image
AlbumArtSmall - 75x75px small version of the above
AlbumArt{GUID}Large.jpg - 200x200px artwork
AlbumArt{GUID}Small.jpg - 75x75px artwork
Thumbs.db - cache of images used by Windows Explorer
where there might be multiple files with different GUID's (Globably Unique IDentifier). Occasionaly the images are not square in which case 200px & 75px will be the maximum dimension. The files are nomally both Hidden and marked as System files which might be why they are not showing.
If you've been letting iTunes or any other program reorganise your music folders then you may have some that are empty of music and simply contain the legacy of WMP's earlier involvement. I've written a script called CleanDeadArt which can be used to tidy these up. For folders that still contain music they won't be doing any harm. WMP will just try to recreate them given a chance. Again the script is fairly easy to modify if you want it to be more aggressive, e.g. remove/archive all artwork, or it could be set to just unhide things so you can see what is going on.
tt2

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