Conversion Software

3D

 * MilkShape 3D

Archives
Refer to Compression and archiving software.

Audio

 * Audacity (cross-platform, open source, website)
 * CDXtract (Windows, Mac, commercial, website)
 * FFmpeg (cross-platform, open source, website)
 * Konvertor (Windows, freeware, website)
 * MediaCoder (Windows, adware, website)
 * SoX (cross-platform, open source, website)
 * SUPER (Windows, freeware, website)
 * VLC (cross-platform, open source, website)
 * WinAMP (Windows, freeware, website)

Character Encoding

 * Iconv (various implementations)

Database

 * Embulk (open-source data transfer utility to exchange data among databases, cloud services, and file formats) (Site, List of plugins)

Document

 * librevenge (Library to make document-format converters, open-source, )
 * MacLinkPlus (68K and PowerPC Mac, commercial, discontinued, )
 * Pandoc (multi-format document converter, specializing in markup and word processor formats, open-source, )
 * WinConv (Windows, commercial, )

Ebooks

 * Calibre (cross-platform, open source, website)
 * Konvertor (Windows, freeware, website)

Encryption

 * OpenSSL

Graphics
Refer to Graphics software.

Interactive Fiction

 * scott2zip (cross-platform, open source, download)
 * UnQuill (MS-DOS, open source, download)

Miscellaneous

 * Convertio (web-based file converter, website)
 * Online-Convert (web-based file converter, website)

Video

 * FFmpeg (cross-platform, open source, website)
 * HandBrake (cross-platform, open source, website)
 * Konvertor (Windows, freeware)
 * MediaCoder (Windows, adware, website)
 * MiniTool MovieMaker
 * SUPER (Windows, adware (installs lots of annoying toolbars and stuff), website)
 * VirtualDub (Windows, open source, website)
 * VLC (cross-platform, open source, website)
 * WinFF (cross-platform, open-source, website)