None of these are in any particular order. I do have preferences, but I'm not going to try and determine them right now. Also, these reviews aren't IMO particularly good. I can go into more detail if prompted.

Favorite 1999 releases:

Olivia Tremor Control - Black Foliage Volume I
The criticism probably most often leveled against this is that it's too pretentious, that the pop bits and experimental bits aren't miscible. I couldn't disagree more.
Mogwai - Come On Die Young
Here's a gedankenexperiment for you: if I were to kill myself, whatever media types I could attract would head straight for my Marilyn Manson CDs, instead of this. Fools. Marilyn Manson would kill himself if he were in the right state of mind, and listened to too much Mogwai.
Waits, Tom - Mule Variations
I still don't think it's as good as the classic Rain Dogs era material (doesn't sound as playful), but it's still good. In particular "Chocolate Jesus" and "Georgia Lee" are favorites.
Low - Secret Name
Years of obliquely-hinted-at violence comes bursting to the surface. But, with it - fiery joy. I'm not fond of Albini's production work compared to Steve Fisk's on The Curtain Hits the Cast, but it's still quite nice.
Godspeed You Black Emperor! - Slow Riot for New Zer0 Kanada EP
"Blaise Bailey Finnegan III" is far more charming than you'll let yourself admit at first. Yes, he's obviously crazy. Yes, his argument is full of holes. But once he really gets going, it sounds so believable... The music is the key. Any old schmuck like Blaise would be passed over immediately, without the emotional intensity of the music to back up the ranting.
Bonnie 'Prince' Billy - I See a Darkness
He makes hillbillies seem so interesting...
American Analog Set - The Golden Band
Played quietly, it's like a gentle lullabye. At higher volumes, the organs, vibes, and guitars (especially bass guitar) create an astounding wash of pure warmth. The central portion of the album is subtle - it can pass by with the listener completely oblivious to the passage of time. Another notion of what "psychedelic" can mean.
Labradford - E luxo so
It's become my favorite Labradford album, if only because it doesn't make funny noises in my CD player like _Mi media naranja_ does. But where that album is far more lush, _E luxo so_ is nothing if not subtle. Unlike some other minimalistic music (like Pan Sonic's A, which I group it with in my head), which approaches its goals by starting with the bare rudiments of sound, then building up toward music, this album starts with ("normal") music, then pares it down.
Autechre - ep7
Familiar Autechre goings-on, only beneath a layer of murk and subterfuge. Many of the songs here sound vaguely related to those from, say, LP5, in the way a wax model resembles the same model, later melted in the sun. Thus, ep7 isn't as immediate as LP5 or tri repetae++, but it's still rewarding.
Mojave 3 - Out of Tune
The pictures of the beach, and the reference to the Mojave desert, are apt. The music recalls: a sort of warm-faced heat; dusky reminiscences; a 3AM drunk.
Red Stars Theory - Life in a Bubble Can Be Beautiful
Will probably end up being criminally ignored this year, despite its worth and probable appeal to fans of bands like Mogwai. Long, sad, droney songs about nothing in particular: just what your favorite indiekid ordered for Christmas.
Stereolab - Cobra and Phases Group Play Voltage in the Milky Night
I almost never listen to the whole album in one sitting, but that's just a sign that it's a little long. The music's still good. Nothing earth-shattering as far as Stereolab goes, but still good.
Burning Airlines - Mission: Control!
THE most criminally ignored album of the year. Two former Jawbox members (Bill Barbot taking Kim Coletta's spot at bass) and a new drummer. The songwriting here has improved immensely over that of Jawbox - it seems they've finally wed their pop tendencies to the kind of DC hardcore they like. Each song on this album is almost immediately memorable, and each has a lot to offer: skittering rhythms, lockstep interplay between band members, thumping, booming, rubbery basslines, sharp, crisp guitar parts... The lyrics are in keeping with Jawbox's past work, if perhaps a little less esoteric. Much like Fugazi's, though, they're sung sometimes contrary to normal diction, instead fit to the music. Once deciphered, though, they're eminently satisfying, much like the CD as a whole.
Wilco - Summer Teeth
I became enthralled by this briefly during the summer, then set it aside. I have no idea why. Revisiting it at the end of the year, I'm reminded how beautiful it is: wry, wistful, complexly emotional. Especially the centerpiece, the three tracks "Pieholden Suite," "How to Fight Lonliness," and "Via Chicago."
Miles Davis - Bitches Brew (Remaster)
If you like modern music, you owe it to yourself to purchase this fine, fine remaster, which makes the old CD version sound like it was recorded beneath mounds of fluffy pillows. The music? Astounding. Miles never reached these heights again.

Also notable:

Jawbox - My Scrapbook of Fatal Accidents
A collection of live cuts, B-sides, covers, and rarities that helps elucidate what was special about Jawbox.
Elf Power - A Dream in Sound
I don't find this as impressive as the other Elephant 6 albums I love (OTC, NMH), but it's still, somehow, found a way onto my list. Comparisons to the Flaming Lips seem inevitable, and I'm still sorting out what it is that's different about them and Elf Power. Worse tasks could fall to me, since I'll have to listen to lots of Elf Power and Flaming Lips in order to unravel the mystery.
Roots, The - Things Fall Apart
I'm not a big hip-hop fan, simply due to nurture vs. nature. I'm slowly working on rectifying that, though, and the Roots are helping me do it. For me, standouts include "Act Too (Love of my Life)" and "You Really Got Me."
Tricky with DJ Muggs and Grease - Juxtapose
"I Like the Girls" is about lesbians. QED.
Rachel's - Selenography
Yes, Rachel's has found another way that classical, art music and "rock" can intersect. People from both camps should take note.
Pan Sonic - A
The most astonishing thing about A, for me, is how vital and musical it sounds, when I really listen. More full of life than a hundred cookie-cutter alternarock bands, and that done only with the sort of sounds you'd think it bad for your household appliances to make.