The way I typically see this implemented is via a Hierarchy custom setting.
Create a custom setting of type hierarchy called Trigger_Disabled__c. Then you can create Account_Disabled__c, Contact_Disabled__c etc fields on it for the particular sobject instances you need to disable.
Why a hierarchy setting? You could use list custom settings as well, but if you wanted to disable workflows or validation rules as well, you can reference hierarchy custom settings in formulas.