Questions regarding a particular region or university
X vs Y questions with subjective answers. Like "Where do I get my PhD from USA or Europe"
As is, it's too broad. With more specifics it may actually be interesting, and in my opinion should stay open.
List Questions like "Labs which do Machine Learning"
Too broad, but if more specific it definitely should stay open. If I want to find the academic expert in one sectorial topic, this SE is definitely the place to go.
Software pertaining to Academia (Mendeley or otherwise)
Predicaments one gets caught into. Like "My advisor is leaving his job and I'm in 5th year of PhD"
Absolutely yes. Such questions may involve legal and administrative issues requiring others' experience to navigate. This SE is about navigating through the jungle. These situations are the trees. If you stay in the savanna, the whole thing is a mere exercise in time-wasting.