SUCTION PRINTS, by far. It's in his 5 most complex songs.
My top 10 would be:
1. SUCTION PRINTS
2. Hair Pie
3. One Red Rose That I Mean
4. Dali's Car (beautiful study in disonnance)
5. Peon
6. Ice Rose
7. Evening Bell (this is his most complex piece for guitar only, it's not very melodic, but just hearing how Gary Lucas put it together is nuts.. basically, Don played an ALL OVER THE PLACE piano piece for two minutes, randomly banging on keys, truely 100% random. Gary decided to transcribe it. He worked out 10 seconds a week. It's a 120 second track, so it took 3 months to get down perfectly. And it shows, because this thing is complex as hell -- and there are videos on youtube of him playing it note-for-note perfectly, which is unbelievable. The way this thing jumps around is nuts)
8. Semi Multi Coloured Caucasian
9. A Carrot is as Close as a Rabbit Gets to a Diamond (might be better if it was in tune)
10. Alice in Blunderland (that guitar solo ruins it imo)
Can't forget the 9 minute SPITBALL SCALPED A BABY, an instrumental only performed live.
Instrumentally, his best songs were
1. Thousand and Tenth Day of the Human Totem Pole (the most complex song ever recorded by a rock band)
2. Sheriff of Hong Kong (see above... the bass and the drums lock into this one in INSANE grooves and rhythmic switches. Just un fucking believable)
3. Frownland (while this has never been one of my favorite songs, if you listen closely it's clearly the most complex song on Trout Mask, there are no 'touch points', so everyone kinda plays to a pulse, very strange)
4. Odd Jobs (after a minute of vocals, the next 4 1/2 minutes are vocal-less and feature the most insane guitar interplay ever)
5. Steal Softly THru Snow (this one totally rocks but there's literally about 30 riffs on it, it is hell to play perfectly)
6. Best Batch Yet (another one that must be hell to play, there are 3 guitars on this piece, and the way them and the bassist switch notes is impossibly complex)
7. Making Love to a Vampire With a Monkey On My Knee (ack! There's so much going on.)
8. When I See Mommy I Feel Like a Mummy (see above)
9. The Clouds are Full of Wine (just that bass/guitar/marimbo intro alone, probably the craziest little 30 seconds of musical interplay in a Beefheart song; also see "Bellerin' Plain" from the same album)
10. Doctor Dark (EVERY instrument is playing in different time signatures, and then the guitar begins to slow down, and all the other instruments slow down and lock time with it but it still remains awkward, the drums do a loooong roll and suddenly EVERY instrument is together. Then they break apart again and all go in completely different directions. Then they lock back in. Is the only Beefheart song with a pretty noticeable guitar mistake in it, in the middle, as Zoot shifts from a weird "Solo" to a part where he plays single notes perfectly locked to the bass and the hi-hat, I like this mistake because it makes the song seem less robotic and really reinforces the fact that this fucking song is hell to play. Instrumentally, LICK MY DECALS OFF BABY is thier most insane album)
Which is why I have a treat for you all..
http://www.mediafire.com/?jtmtyotwdmy
LICK MY DECALS OFF BABY: INSTRUMENTAL.
Yeah, seriously. It's the entire DECALS album, some are the versions you've heard but instrumental, some are versions you never heard, instrumental (keep in mind the ACTUAL instrumental songs aren't on here). 18 songs long. Lots of goodies. So, this might be just what you were looking for, DISCODILDO!
I gotta say, they should've probably kept FLASH GORDON'S APE an insturmental, and took out the horn. On the actual version, the mixing is stupid, the horn is in the extreme left and LOUD, the band is in the extreme right and quiet, and the vocal is louder than both (actually, that whole album really needs remastered, it sounds pretty thin and ugly and there's so much going on that is hard to hear; SMITHSONIAN INSTITUTE BLUES has 3 guitars, a bass, a marimba, two drum tracks, and vocals... it's a great song but it's scuh a mess with that shitty production. It reminds me of the production of sister.. the songs are so good that it doesn't matter, but it's in DESPARATE need of a remaster!!!!!!!).