This is really too broad of a question to answer in any useful way. The most widely used tools for molecular identification in an analytical lab would be mass spectrometry (MS), possibly interfaced with some form of chromatography. But there are dozens of varieties of MS, each one suited for particular types of analyses. The particular method you would use in any given circumstance would be specific to the type of chemical, the matrix, the precision/accuracy requirements, the likely concentration, and so on. Supplemental methods might be needed also depending on what information you need and how much information you are starting with. There are few occasions where a single method will do everything you need to do.
It's also worth pointing out that amateurs and students often assume that modern chemistry is a field where the analyst is presented with a blob of unknown stuff and tasked with determining what it is made of. In reality, though, this is not what most chemists do on a daily basis. Although some fields certainly require chemists to engage in detective work starting from a blank or nearly blank state, in most cases analytical chemists have an idea (or know exactly) what they are looking for, and most problems are more centered around sorting out the signal from the noise (which involves both chemical purification and managing analytical interferences), measuring accurate concentrations, or confirming that they do indeed have what they think they have. The modern chemical toolset is oriented accordingly around targeted rather than black box analysis.