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If you are talking about an AC mains power transfer, the choice depends on the purpose for the tap.
- Tapped primary accommodates different AC mains voltages, such as 100, 120, 240.
- Tapped secondary generates different output voltages.
You might get away with using taps incorrectly, however you could get lower efficiency (greater heating), and you must be careful not to exceed the transformer's voltage and current ratings, or saturate the core.
Personally, I like the primary taps, since I build powersupplies a lot. It is handy. Instead of needing 2 or 3 different transformers, you can use one with the multiple taps.
Same for the secondary. I usually buy the ct types, again for the same reasons above.