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They use signatures. You can see the logic Detect-It-Easy uses to detect each tool by looking at the appropriate script https://github.com/horsicq/Detect-It-Easy/tree/master/db/PE
A signature-based approach with YARA can work to fingerprint the specific software used to obfuscate the malware. A lot of YARA rules for a variety of purposes can be found here, and it might be useful to aggregate ones you care about into your own little detection pipeline.
As others have mentioned, looking at entropy is a good metric to generically determine whether or not a given sample is being packed / obfuscated in some way. Doing static analysis on the binary format itself (I'm assuming PE for Windows is the goal) is also useful, such as checking whether or not a section's raw size on disk is much smaller than the virtual size allocated in-memory for that section, which is a reliable indication of packing behavior. This project looks useful for introspecting such behaviors.