Some old classical DOS games are still for sale as downloads. Lets collect links for these in this thread for those of us who just want to have their own legitimate copies of favorite games in easy way and don't care so much about hunt for physical packages.

http://www.idsoftware.com/store/index.php?view=downloadable
ID Software store.
All games repackaged in one-file Windows installers (Win9x compatible). DOS games doesn't contains DOSbox as "wrapper". Doom series (and Hexen?) is Windows versions here.
Return To Castle Wolfenstein
Quake
Doom
Doom II
Final DOOM
Heretic
Hexen
Wolfenstein 3D
Spear Of Destiny (2 additional "official" 3rd party episodes included)
Commander Keen: Invasion of the Vorticons and Goodbye Galaxy Set (1-5, Aliens Ate My Baby Sitter is not included. All five games in one folder)
Price: 10-20$

http://www.buy3drealms.com/
3D Realms Store.
All games repackaged in one-file Windows installers (Win9x compatible).
DOS games contains DOSbox as "wrapper".
Balls of Steel
Blake Stone: Aliens of Gold
Commander Keen: Invasion of the Vorticons
Commander Keen: Goodbye Galaxy
Cosmo's Cosmic Adventure
Crystal Caves
Death Rally
Duke Nukum (The Original)
Duke Nukem II
Duke Nukem 3D: Atomic Edition
Duke Nukem: Manhattan Project
Hocus Pocus
Math Rescue
Monster Bash
Mystic Towers
Paganitzu
Planet Strike
Raptor: Call of the Shadows
Realms of Chaos
Rise of the Triad: Dark War
Secret Agent
Shadow Warrior (Despite the warning that download version doesn't have CD music in any form at all, that version contains CUE+OGG group of files with full sountrack. Working in DOSbox only in this form)
Terminal Velocity
Wacky Wheels
Wolfenstein 3D
Word Rescue
Price: 5.99-10$

http://www.virtualsoftware.com/
Reseller. Contains many old and simple DOS & Win16 games. Mostly puzzle & logical. Interesting is Flat Rock Software (ex. Softdisk, most of it made by ID Software) and DISCo (ex. Gamos) titles.

Softdisk / ID Software (looks like there is original unchanged Softdisk installers for DOS):
Dangerous Dave in the Haunted Mansion
Dangerous Dave's Risky Rescue--Dave Returns!
Dave Goes Nutz
Keen Dreams
Catacomb 3-D
Catacomb Abyss 3-D
Catacomb Apocalypse
Catacomb Armageddon
Hovertank 3-D
Rescue Rover
Rescue Rover 2
Shadow Knights
Slordax
Price: 10$

DISCo (ex. Gamos):
Balda v1.0
Branch v1.0
Columbus Discovery v1.0
From Corner to Corner v1.0
Kalah v1.0
Life Editor v1.0
Magnetic Labyrinth v1.0
NetWalk v1.0
Nine v1.0
Patience v1.0
Picker v1.0
Regatta v1.0
Sabor v1.0
Snake Battle v1.0
Wild Snake v1.0
Price: 10-15$

http://www.mking.com/downloads.htm
Mountain King Studios Inc. (ex. Cygnus Studios) games.
Price: 9.95-19.95$

http://www.gog.com/en/frontpage/
G.O.G means Good Old Games. Reseller. Has some old DOS gems. Games packaged in one-file stylish executable installer. Unfortunatelly is incompatible with Win9x at all. Even for DOS/Win9x games, what a shame!
Price: 5.99-11.98$

http://store.steampowered.com/
Steam. There's no DRM for DOS games.
id Super Pack
Space Quest Collection
King`s Quest Collection
The Dig
LOOM
Indiana Jones and the Last Crusade
Indiana Jones and the Fate of Atlantis

Who knows more, please?