In Dungeon Crawl Stone Soup — in the early game, the midgame, and the endgame — which spells are most often memorized by winners?
In the early to mid-game: Mephitic Cloud. You can also use Passwall to escape monsters through 1-thickness walls.
All game long: Blink, Apportation, Swiftness, Repel Missiles, Regeneration, Animate Skeleton, Summon Butterflies, and Flight.
As soon as you can cast them reliably: Control Teleport and Haste.
See the aforementioned wiki article: it includes much more information. This includes information on direct-damage spells, plus a link to the raw endgame spell-popularity statistics.
This post is up-to-date for Crawl 0.14. Please edit the wiki article and this post, and add to them. If you'd like me to mark this answer as community-wiki, please comment and request it.