You are most likely thinking of the ultra-violent "Brain Thieves"!

If you haven't seen it and would really like to, you'll just have to lay hands on a copy of the Black DVD, the one with the Good Skellington, the Bad Skellington and Hannah the Human on it.

The Surgical Sideshow had been invited by
Juke Baritone and the Swamp Dogs to spice up their Halloween set
at the Famous Spiegeltent by the Sydney Opera House
on the 31st of October, 2008
Excited by the prospect, the Skellingtons thought it was time to tell a story they had been saving for just such an event.
The Surgical Sideshow performed while the Swamp Dogs played to the drama.
Ever since, this episode has been performed as a "musical" of sorts and Hannah was the first Human to do it.

For the recording of this episode, a replacement musical backdrop was used, which was to soon provide for future performances. This also allowed for the usual range of odd sounds and strangenesses to be added. However, as a nod to the original intention, every performance has used a live police whistle.
The first performance with this new soundscape might be the one you saw
for the Night of Horror film festival and special presentation at
Club 77 in Kings Cross
on the 29th of March, 2009

Juke and the Swamp Dogs were playing at a fundraiser at which, coincidentally,
the inhabitants of The Surgical Sideshow Puppet Theatre were acting as comperes.
Strings were pulled, favours were called in and The Surgical Sideshow joined them onstage for a re-enactment performance,
at the Oxford Art Factory in Darlinghurst
on the 9th of April, 2009

Perhaps you were amongst the lucky crowd to receive the gift performance, the first to follow the initial season of the Surgical Sideshow Epic,
at Planet X in Chippendale for their annual Day of the Dead gathering
on the 2nd of November, 2009.

Hannah was replaced by the wonderful Sha of Bohemian Love Theatre as the Human for the performances
at the Peats Ridge Festival
on the 29th and the 30th of December, 2009.

Perhaps you saw these ones! Three episodes were performed each night, on the purpose-built Surgical Sideshow Stage. These were interspersed with brief sets by the talented Lanie Lane and Dangerboy.

Doesn't that sound familiar to you?
There's still hope, you might have seen something else.