If you want to do it the long, slow way you can just add more rules to your str_replace.

I may have gotten the regex wrong for the bbcode. It's tricky to know which characters to escape and trying to do them as a character sequence may not work. may be easier to do it like (\<|\[) and change the backreference.
ie.

$content=preg_replace("@(\<|\[)spoiler(\>|\])(.*)(\<|\[)\/spoiler(\>|\])@simU","<span class='spoiler'>\\3</span>" , $content);

And now that I look at it, if I use [\<\[] that leaves the door open for some silly person to do this and have it work:
<spoiler>neener![/spoiler]

While that's kinda okay, it's also kinda not (bad HTML among other things). The preg_replace solution has the same problem, while it's certainly simpler.

this is wrong:
<span class="spoiler">[spoiler]Test?[/spoiler]</span>

should just be:
<span class="spoiler">Test?</span>

Actually, the entire way your plugin works is overly complex.

You could do the whole thing with one preg_replace.

$content=preg_replace("|(\<\[]spoiler[\>\]])(.*)([\<\[]\/spoiler[\>\]])|simU","<span class='spoiler'>\\2</span>" , $content);

(untested)

The trunk is available for testing: http://plugins-svn.bbpress.org/spoiler-bar/trunk/spoiler-tags.php

If someone who uses BBcode would be so kind :)

function bb_spoiler( $matches )
{
        $text = $matches[0];
        $text = str_replace("<spoiler>", "", $text);
        $text = str_replace("</spoiler>", "", $text);
        return "<span class=\"spoiler\">$text</span>";
}

And naturally I'm not using BBcode so I can't easily test that myself. I suppose I could uglify it and make separate bbcode functions but I'll go play with regex cause that would be better ;)