Again, I grabbed these from Pikachuchu's blog (as she was far quicker off the mark in cataloguing this whole thing than me), which you can visit at: http://hellboyfilm.over-blog.com/
In brackets after each I've put a couple of comments, most of them are just speculation and should be treated as such.
An abomination hath been done,
The wheels of motion turned and spun,
A quarter moon past,
Time runneth fast,
Our countdown already begun.
(The original limerick, which seems to infer nothing more than that we are to keep an eye on the site. Which we did.)
Rise up prepare to act,
The future is bleak in fact,
Unite as one,
Oh earthly son,
Protect the ancient pact
(Again, this one seems to just be an indication that we are to keep watching the site - as they can, and did, make updates and changes.)
From light they often make stone,
Time for us all to atone,
Years of abuse,
From persons obtuse,
One nine of a month yet unknown.
(This one seems to indicate a date - one nine of a month yet unkown (i.e. the 19th of something) - which makes no sense until the fifth limerick)
A very dark day in our prime,
Our planet is covered in grime,
Pray hear our concern,
All ye to learn,
Five plus one less than a dime.
(This one gives us another sum, which comes to 14 - as of yet we've had no use for it.)
Four out of twelve leads the way,
Twenty less one points the day,
Of primary concern,
For thou to learn,
Fine creatures are dismay.
(This one was easy and fairly explicit - four of twelve, well that's months, so April. Twenty less one, that's 19. April 19th. When we went back to HETFET on April 19th, it had opened!)