This is just a quick (and non-exhaustive) list of tools that I use to tag various system objects:

• To tag files: Fresh;
• To tag photos (in iPhoto): Keyword Manager;
• To geotag photos: HoudahGeo;
• To tag email messages (in Mail.app): MailTags;
• To tag bookmarks: delicious.com.

Stay tuned, I will review these and other applications in the coming weeks.