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Harmful software, with less harmful alternatives.

Bash, tcsh, mksh. -> ash/dash. -> rc, pdksh.
Coreboot. -> Libreboot.
C++, Java, Python, Ruby, -> Go. -> C.
GCC. -> 8c, tcc.
Git. -> darcs.
Glib. -> libc
glibc. -> musl, ucLibc, DietLibc.
GNU autoconf/automake, CMake, imake, scons, waf. -> mk, makefiles.
GNU Coreutils. -> Plan 9.
GNU info. -> Man pages.
GNU Screen. -> tmux. -> mtm.
GPL, LGPL, Apache Software License, MPL, CC, ISC, MIT/X, BSD. -> public domain. -> CC0.
GTK, Qt. -> Tk, textual interfaces.
HTTP, -> Gemini, Spartan. -> Gopher.
IMAP. -> SMAP.
JPEG. -> GIF. -> PNG.
LBRY. -> Peertube. -> GNU Media goblin.
Links, w3m. -> Lynx.
Linux, FreeBSD. -> NetBSD. -> OpenBSD.
mini_httpd, darkhttpd, thttpd. -> Don't use HTTP.
Neocities. -> Pubnix. -> Self-host.
NFS, SMB, AFS. -> 9p.
PDF, EPUB. -> PS, DjVu.
Perl, Ruby. -> rc, awk.
SGML, XML, YAML. -> JSON, CSV, -> Plain text.
SVG -> PS.
SQL databases. -> Tutorial D, pq, BigTable, hierarchical filesystems.
Tor, Lokinet. -> I2P.
UTF16. -> UTF8. -> us-ascii.
Vim, Emacs. -> vi.
XMPP. -> IRC, STOMP.