You need to use the square brackets notation to have values sent as an array:
<form method='post' id='userform' action='thisform.php'>
<tr>
<td>Trouble Type</td>
<td>
<input type='checkbox' name='checkboxvar[]' value='Option One'>1<br>
<input type='checkbox' name='checkboxvar[]' value='Option Two'>2<br>
<input type='checkbox' name='checkboxvar[]' value='Option Three'>3
</td>
</tr>
</table>
<input type='submit' class='buttons'>
</form>
Please note though, that only the values of only checked checkboxes will be sent.