As Crawl is an actively developed game, features are being added and removed all the time. When a feature is largely no longer present in-game, it can be said to be obsolete. It should be noted, however, that a feature which is 'obsolete' may not be entirely removed from the game. The term can apply to a variety of conditions. Some examples are given below:
These are features that have been entirely purged from the code, and are not present in any way, shape, or form. The obsolete spell Alter Self falls into this category. Most removed items will as well, as they are relatively simple to remove entirely.
This category describes features which are removed and not present in-game, but for which some code remains. There are a variety of reasons that this may be the case. In some cases, most notably with the removal of species, the developers will choose to wait until the next major version to entirely remove the race, so as not to break compatibility with old saves until absolutely necessary. In other cases, the persistence of code for a feature may simply be due to developer oversight or choice. An example of this is some removed tiles, which are present in the rltiles/UNUSED directory of Crawl's source folder.
This describes features that are mostly gone, but still present in some very reduced form. A good example of this would be the spell Orb of Electrocution. As a player-castable spell it was removed in 0.1, but it still remains as a potential effect of Makhleb's Greater Destruction.
No longer available to the player
This is actually a fairly large category, mostly with spells. Many monster spells, such as Paralyse, Haste, Repel Missiles and even self-healing spells, were once player spells. They are obsolete in the sense that the player can no longer use them as spells, but they are by no means gone from the game, and their effects may even still be available to the player through non-spellcasting means.
Whether a game concept is removed from the game or simply given a fresh appearance, much of the artwork which has been created for DCSS is no longer available in-game. You can find an archive of retired artwork here.