When planning a session or adventure, obviously one should take into account the approximate power level and capabilities of the players. For creatures and similar formal challenges, CR helps scale the difficulty of an encounter. However, as the PCs progress, they may gain capabilities that make situational challenges easy or even trivial. For example, challenges requiring escape or travel could easily be bypassed once one of the PCs learns Teleport. After learning/suspecting an apparent ally of treachery, Scrying greatly simplifies the process of finding out what they're up to. My problem is that, aside from a few examples, I don't know what to look out for.
How can I avoid being blindsided by significant PC capabilities like these? Note that my question is not about how to circumvent or build around these capabilities. Instead, I would like to know how to see them coming so I can handle with my own ideas. As such, it doesn't really make sense to look at specific examples; the examples are what is desired. Additionally, it's only especially important to consider when they have access to these capabilities from their own power, as the GM can easily avoid providing the PCs with power they are not prepared for.
Ideally, there would be a sort of list of special capabilities players have general access to and at what approximate levels. That is, the list may contain "instantaneous travel that ignores obstacles" or "spying at a distance". A spell compendium is not suitable; there are countless spells that just do damage, or that enhance capabilities acquired earlier. Without some familiarity with all of the spells available, it's not clear that spell X is really the first practical means of achieving some capability. In addition, not all capabilities are spells; consider Wild Shape and other class abilities.
If a list of major capabilities is impractical or not a good StackExchange format, tips for enabling a GM to find these milestones would be appreciated.