I'm not entirely sure what your asking - what do you mean by "custom conditionals" ?
A template conditional is just:
Code:
<if condition="$something"> ...html... </if>
Which in english, translates to "If $something is equal to true, then echo this html".
In your PHP script / plugin / etc, you'd set:
PHP Code:
$something = true;
if you wanted the template conditional to run.
(hopefully that makes sense)