Both lists above are more or less in order. The last three (EF, Hood, AoR) were somewhat disappointing to me, but all the rest is recommended with little reservation.
I don't actually own the Unwound, The Sheila Divine, In Gowan Ring, and Handsome Boy Modelling School, though I own most of the singles that are on that Unwound comp, and I've heard the other three a couple times. TSD would make it in my top 20 on the strength of the two radio singles alone ("Hum" and "Opportune Moment"), plus all the times I saw them play to a half-full Middle East Upstairs (of course now they're selling out the Paradise and touring with Morrissey...)
The Bull-Roarer & Ray Corvair Trio are debut full-lengths from two other great Boston-area bands; the former is stompy burly noise-rock, the latter is smooth spy/surf instrumental. Both have not-to-be-missed live shows.
Charlene is another great local band, Spacemen 3-derivative but in all the right ways (e.g. they stick a weight on a Vox keyboard key while playing their guitars). The 7" is so low on my list because I still haven't actually listened to it-- one of these days I'll unbury my turntable...
Oranger is the current Bay Area psych-pop-punk band of Matt from Overwhelming Colorfast, and anyone who has known me for a few years knows how much I loved them. The Oranger album (more like an EP) is fantastic, with just the right crunch to the guitars and just the right lilt to the harmonies. My copy is actually on Pray For Mojo from '98, but it was reissued on Amazing Grease this year. Other reissues above are Sleep (actually only a bootleg previously), Harmony of the Spheres, Air, Billy Idol (now with demos!), Skip Spence, and Hood.
Other info: Idyll Swords is Dave from Polvo and Chuck from Spatula in a Chapel Hill indiesupergroup, doing Faheyesque guitar stuff along with various permutations of exotic stringed instruments. Atomic Bitchwax is Ed from Monster Magnet's side band, a bit less space-metal and more 70's boogie-rock, but still darn heavy. That Bardo Pond album, I have to say, has probably my favorite song of 1999, "Again", but it's so unrepresentative of what I usually like them for; most of the rest of the album is kind of filler-ish too, which is why it only barely cracked my top 20. The Church album is all covers-- better than those kind of albums usually are. Abunai!, Cathode, Betwixt, and Cul de Sac are all local bands as well. Tabata is Mitsuru Tabata, guitarist for Zeni Geva, doing some nice experimental atmospheric noise stuff. Altamont is Dale from the Melvins's side thing, a silly southern-rock-ish metal album that ends up sounding a bit like Fitz of Depression.
Two records that without a doubt would be on my list if I had heard them are Wayne Rogers's Constant Displacement and Major Stars Space/Time, both on Twisted Village. They are still vinyl-only, but the CD release is imminent (supposedly). Which means they'll be eligible for next year's list, of course... Other records that I would probably have liked if I had heard them include Godspeed YBE, Jim O'Rourke (two 1999 releases!), Chemical Brothers, Dillinger Escape Plan, Crom-Tech, Golden, and Cobra Verde.
I just got a few more records that say 1999, but I suspect were released in the last two or three months, so I'll save them for next year's list: