create a block macro
[% MACRO alt_color(loop_count) BLOCK %]
  [% IF loop_count % 2 == 0 %]
    color1
  [% ELSE %]
    color2
  [% END %]
[% END %]

in your template you do
loop.count is a special property of the iterator
[% FOREACH thing = things %]
  <td class=[% alt_color(loop.count) %]>[% thing %]</td>
[% END %]