What's the best way to track and alert inactivity in opportunity stages?

And added to this, would i need to create custom tags /fields so the alert can be customised to the opportunity? There doesn't seem to be default opportunity tags in Marketo

Hey Erin, 

I would use the "Opportunity Was Updated" / "Added to Opportunity" triggers combined with wait steps.

The idea being that you have a listener campaign that resets the clock each time a status changes and a wait campaign that will send the alert if nothing happens.  This will form an iterative loop. I would cap it off with a campaign that removes them completely once the opportunity is Closed Won/Lost. 

E.g.,

Listener Campaign

SMART LIST
Added to Opportunity
Opportunity Was Updated - Stage (new value is not Closed Won/Lost)

FLOW
Remove from flow [Wait Campaign]
Request Wait Campaign

Wait Campaign

SMART LIST
Campaign is Requested

FLOW
Wait [your max # of days]
Send Alert

Closed Campaign

SMART LIST
Opportunity is Updated - Stage is Closed Won or Closed Lost

FLOW
Remove from Flow [Wait Campaign]

This will work well unless there are multiple open opportunities at a time. Marketo won't be able to distinguish them. You could also try doing this via a Process or Workflow Rule in SFDC, which may make it easier to work with multiple open opportunities. 

With respect to the email alerts, you would have to use email scripting:

https://community.marketo.com/MarketoArticle?id=kA050000000LB9MCAW