The vocals on The Catalyst use the Waves Metaflanger VST plugin.
Several guitar samples from the same MPC sample bank were later used in Bruiser and Victimized. The majority of the distorted guitar work in Wretches and Kings consists of a bunch of guitar samples recorded by Brad that Mike chopped up and played with an MPC.
Mike sat next to Brad while Brad was recording the solo and rhythmically flipped the Expression switch on the HOG on and off, creating the sweeping sounds heard on the album. The guitar solo on Waiting For the End uses a multi-octave splitting effect on an Electro-Harmonix HOG. The Spanish lyrics in both Empty Spaces and When They Come For Me come from Brad yelling into a megaphone. They found a way to use them in the song.
The tapping sounds at the beginning of When They Come For Me are actually one of the stock Pro Tools metronome sound effects, which are normally muted out of the final mix. The vocals are Mike's voice run through a vocoder (possibly an Electro-Harmonix V256). The Requiem is largely comprised of samples of other songs found on A Thousand Suns. The keyboard sounds on In Pieces are either a marimba, or a virtual version of a marimba. The melodic guitar figure throughout the song is played with an EBow. The clunky sounds in the background of No More Sorrow (most easily heard in the intro) are the sounds of a broken air conditioner at the Laurel house. The sound at the beginning of What I've Done is a reversed guitar chord. The opening sound on Wake is a needle being placed on a crackly old vinyl record. The flute in Nobody's Listening is a Japanese shakuhachi. Everyone's heard this one by now, but the intro to Somewhere I Belong is a chopped-up/reversed sample of Chester playing acoustic guitar, with some additional effects on it. The banging sounds in Foreword are actually the sound of Mike repeatedly hitting a broken CD burner with a metal baseball bat. The short "swelling" guitar sound at roughly the 3:13 mark is also a clip of the "normal" guitar riff played backwards.
Brad had to learn how to play this after the fact in order to perform the song live.
Mike took a different guitar riff that Brad had recorded, chopped it up, and rearranged it into the "stuttering" riff that wound up in POA. Points of Authority's guitar riff was created artificially in a computer. One Step Closer has a camera shutter sound effect in it (best heard on the original "Plaster" demo). The high-pitched loop in the intro/throughout Papercut is NOT a guitar, but an MPC sample played by Joe Hahn that was run through one of the distortion effects on a Boss GT-5 guitar multi-effects processor. The buzzing noises at the beginning/throughout Part of Me are a looped sample of a car alarm that Brad recorded on a handheld tape recorder at his apartment. The chorus vocals on the Hybrid Theory EP version of High Voltage are run through a vocoder, likely a Music and More VF-11 "Next!" unit, as was used on Intergalactic by the Beastie Boys (which the original version of High Voltage was clearly trying to imitate). This is purely from racking my brain by going through the band's main discography in chronological order, so it's probably missing a lot of stuff I've researched over the years, but it's a start: