When you delete or move a message, most e-mail clients simply hide the message and mark it as ready for physical deletion later on. The “deleted” messages are still stored in the folder even emptying the Trash does not remove them. The hidden messages are not physically removed until the folder is compacted. If you don’t compact your mail folders periodically, they can grow very large and may become corrupt.
To recover disk space and keep your files as small as possible, you need to compact your folders regularly.
If you feel your Inbox is getting larger break it up and make new folders. Use filters for segregating mails in appropriate folders. Check and delete unimportant junk mails frequently.
Procedure to compact folders on
Thunderbird
File -> Compact folder (It’ll compact all folders)
Or
Tools -> Options -> Advanced -> Network & Disc Space -> Compact folder when it will save over 100 kB (It will automatically compact folders)
Outlook Express
File -> Folder -> Compact All Folders
Outlook
File ->Data File Management
it will lead you to Data Files tab on Account Settings
Select .Pst folder which you like to compact
Click on Settings…
Compact Now