There's tons of KLF references in their songs:
"Back to the Heavyweight Jam" is a line from the song "Last Train to Transcentral", one of the KLF's big hits.
The Stadium Techno Experience's cover is a reference to the White Room KLF album. The title may be a riff on their "Stadium House Trilogy".
"Posse" is based more-or-less on a sample of "What Time is Love?" (which is probably the song that inspired Scooter in the first place). "Behind the Cow" samples it directly.
Mind the Gap was the name of a Scooter song, and I think the first track "Killer Bees" is a sample of it?
"F##k the Millenium" was also the name of a KLF song (under the name 2k). In that song, H.P. says something like "I'm Sheffield Dave, also known as the Candyman, also known as the Iceman"...well, the KLF did this phrases too in "Last Train to Trancentral". Candyman is also the name of a Justified Ancients song.
The beginning of "3 A.M. Eternal" by KLF has been sampled a few times, I think "Hello (Good to be Back)" samples it directly.
In "Nessaja" when H.P. shouts "3 A.M.!" it is most certainly a reference to this song. Also, "The K the L the F and the ology" is pretty clear. "All aboard all aboard" is from "Last Train to Transcentral".
"Imaginary Battle" has a "take me, uh-huh" sample from the KLF's "Church of the KLF".
"Weekend" has a few references in the goofier lines - "We are not the monkees" was the name of a song by the Justified Ancients of Mu Mu (which is another name of the KLF), as is "Respect to the man in the ice cream van" - the KLF used to drive an ice cream van around.
"Let Me Be Your Valentine" has a brief sample of "Last Train to Transcentral".
The crowd noise in the tracks is likely a reference to the first half of the White Room KLF album which used the same trick. I am somewhat confident (but not 100%) that the KLF were the first ones to do this, and if not I am 100% sure that it was the KLF's usage that inspired Scooter to do it.
I'm sure there's many others too, so get to it!
Edit: As far as I know Ratty isn't a reference