For non AMD files, you need to use shim config. Since parse-min exports it's functionality via global variable 'Parse', you need to specify the global variable name in shim config as shown below. Since bootstrap does not export a particular global variable, you can use any of it's plugin global variable such as $.fn.popover.
For more info on shim config, please read this : http://requirejs.org/docs/api.html#config-shim
require.config({
paths: {
jquery: 'libs/jquery/jquery-min',
underscore: 'libs/underscore/underscore-min',
backbone: 'libs/backbone/backbone-min',
bootstrap: 'libs/bootstrap/bootstrap-min',
parse: 'libs/parse/parse-min',
templates: '../templates'
},
shim: {
parse: {
exports: 'Parse',
deps: ["jquery"]
},
bootstrap: {
exports: '$.fn.popover',
deps: ["jquery"]
},
backbone: {
deps: ['underscore', 'jquery'],
exports: 'Backbone'
},
underscore: {
exports: '_'
},
jquery: {
exports: '$'
}
}
});