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HK eTransport is the government's own transport app, quite useful as i find it has a relatively large database of POIs and lists most if not all forms of public transport in HK, comparable in usefulness with Citymapper in a more mature city e.g. London
Webapp / Mobile Web / iOS / Android
MTR Mobile is the app for the region's train/subway system useful for telling you where to change trains/travel time.
There's always Google maps which is also quite useful in terms of transport directions in HK