HORIZONTAL MOUNTS - Subaru, part number soa521g305
VERTICAL MOUNTS - Yakima Mighty Mount 3V

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Original Post:
I was able to locate 1 set of horizontal mounts for my stock first gen legacy wagon roof rack. I found them at Rack & Road in Seattle, WA. It was a lucky find because they had just been sitting in a back room for the longest time, unmarked, and nobody there even knew the part number or manufacturer. I've got 2 more Yakima bike racks that I'd like to throw on my roof, but need to find out who made these things, and the part number. The guys at Rack & Road seemed to think that they were actually made by Subaru?
EDIT: After more searching I discovered that they were in fact made by Subaru. Their part number is soa521g305. Unfortunately, I ordered the last 6 that existed in Subaru's inventory. I'm unsure if they come in sets of 4, or individually. If they arrive as 6 sets of 4, I'll sell the ones I don't need here on LLC at cost. I'm sure more of them exist out there, but they're going to be tough to find.
NOTE: There isn't really any room to get tools under the roof rack when installing the mounts. I had to fabricate my own stand-offs (tube steel) and bolts (all-thread rod + nuts) due to the super low clearance of the stock roof rack. Drilling a hole in the tire track of the bike rack was also required.
Subaru part number soa521g305
Subaru part number soa521g305 - Installed w/ custom standoffs for additional clearance.
FYI - I was also able to get the vertical mounts at Rack & Road (ordered from their their Utah store). They're Yakima Mighty Mounts 3V. Unfortunately I cannot stack skis or boards due to the super low clearance of the stock rack, I might try and fabricate some kind of riser for them. Otherwise, the bindings on many skis will actually touch or hit the roof. Low profile bindings might not be an issue.
Yakima Might Mounts 3V
Yakima Might Mounts 3V - On Crossbar
Yakima Might Mounts 3V - Installed
Yakima Might Mounts 3V - Instructions

My Legacy did not come with the factory roof rack. I actually got the factory rack at a pull-a-part yard for $15 and was able to get it installed for $75 with a no-leak guarantee. I also had it installed about 10" further forward than the way it came from the factory so that skis and bikes wouldn't get in the way when opening the back hatch. I had 4 Yakima bike racks and a ski rack handed down to me from my parents, and wanted to keep my Legacy as stock looking as possible, so this was the best route. All-in-all, much cheaper than buying all new gear.
It turned out to be a pretty big hassle to get all this stuff to actually work, but I had time on my hands and really wanted the factory rack. If you don't have the factory roof rack, just go with an aftermarket setup, it'll save you a lot of hassle and you wont need to search for these hard to find mounts. If you do have the factory roof rack and want to use it, I think the Mighty Mount 3V's will be a bit easier to find than the Subaru soa521g305's.