The term 90 day limit refers to the fact that once 90 in-game days have passed, the background corruption per turn rate doubles. Places that have not previously corrupted the player, such as the wilderness, the Village Dungeon or the Unremarkable Dungeon, will remain harmless; places that corrupted only lightly will still not corrupt much. The effect is most noticeable in the deeper areas of the Caverns of Chaos and other end-game locations - if sources of controlled teleportation are available in large abundance, it may be wise to minimize the amount of turns spent there by teleporting from stairs to stairs on passing through.
To a beginner, this shift may sound worse than it often turns out to be. With the guaranteed scroll of chaos resistance that can be obtained within the game, and the Unicorn quest, one would have to play very, very carelessly to get into deep, game-ending trouble with corruptions. Still, it increases the rate at which scrolls or potions must be used to remove troublesome corruptions, such as stiff muscles or mana battery.
For those that plan ultra endings, especially a non-lawful one, or ordinary chaos god endings this is more of an issue, as more time will be spent in highly corrupting locations. It is still not terribly worrisome as Khelavaster must be saved for an ultra anyway, and his six scrolls go a long way. Plus, contrary to normal victories, being as corruption-free as possible to ensure a better ending after leaving the chain is not a factor in an ultra ending. Non-lawful PCs going for ultra need to pass the Chaos gate with full set of corruptions anyway, so the problem is the same as for regular wins with annoying corruptions early on.
If the player intends to avoid the onset of the 90 day limit, it is important to realize that by far the most time is spent in the wilderness. Repeated travels between locations, for instance back and forth from the Caverns of Chaos and the Terinyo area or the Tomb of the High Kings valley can eat a lot of time. This factor can be nearly eliminated entirely by some class powers and/or wearing blessed seven league boots, which is part of what makes these so popular.
Note that with the release of ADOM 1.2.0, background corruption will increase every 90 days by the base rate instead of just once—past 180 days, background corruption will be three times higher than normal, past 270 days, four times, and so on.