Solución angular:
HTML
<!doctype html>
<html ng-app='app'>
<head>
<title>
</title>
<link rel="stylesheet" href="http://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap.min.css">
<link rel="stylesheet" href="style.css">
</head>
<body ng-cloack>
<div class="container" ng-controller='FirstCtrl'>
<table class="table table-bordered table-downloads">
<thead>
<tr>
<th>Select</th>
<th>File name</th>
<th>Downloads</th>
</tr>
</thead>
<tbody>
<tr ng-repeat = 'tableData in tableDatas'>
<td>
<div class="checkbox">
<input type="checkbox" name="{{tableData.name}}" id="{{tableData.name}}" value="{{tableData.name}}" ng-model= 'tableData.checked' ng-change="selected()">
</div>
</td>
<td>{{tableData.fileName}}</td>
<td>
<a target="_self" id="download-{{tableData.name}}" ng-href="{{tableData.filePath}}" class="btn btn-success pull-right downloadable" download>download</a>
</td>
</tr>
</tbody>
</table>
<a class="btn btn-success pull-right" ng-click='downloadAll()'>download selected</a>
<p>{{selectedone}}</p>
</div>
<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.0/jquery.min.js"></script>
<script src="https://ajax.googleapis.com/ajax/libs/angularjs/1.4.8/angular.min.js"></script>
<script src="script.js"></script>
</body>
</html>
app.js
var app = angular.module('app', []);
app.controller('FirstCtrl', ['$scope','$http', '$filter', function($scope, $http, $filter){
$scope.tableDatas = [
{name: 'value1', fileName:'file1', filePath: 'data/file1.txt', selected: true},
{name: 'value2', fileName:'file2', filePath: 'data/file2.txt', selected: true},
{name: 'value3', fileName:'file3', filePath: 'data/file3.txt', selected: false},
{name: 'value4', fileName:'file4', filePath: 'data/file4.txt', selected: true},
{name: 'value5', fileName:'file5', filePath: 'data/file5.txt', selected: true},
{name: 'value6', fileName:'file6', filePath: 'data/file6.txt', selected: false},
];
$scope.application = [];
$scope.selected = function() {
$scope.application = $filter('filter')($scope.tableDatas, {
checked: true
});
}
$scope.downloadAll = function(){
$scope.selectedone = [];
angular.forEach($scope.application,function(val){
$scope.selectedone.push(val.name);
$scope.id = val.name;
angular.element('#'+val.name).closest('tr').find('.downloadable')[0].click();
});
}
}]);
ejemplo de trabajo: https://plnkr.co/edit/XynXRS7c742JPfCA3IpE?p=preview