If you look at the scene long or often enough, you can tell it's the Orpheum theater in Vancouver, aka the "Opera House" from BSG. Both the lobby and the theater area are used. This is confirmed in the episode commentary. I made it to Vancouver for a tour of the theater, so here's a pic:
This is the Iona building at the University of British Columbia. Here's a picture I took when I visited:
It's been pointed out in several forums that this is the Granville Skytrain Station:
The next location was a tricky one... Joseph's location during the MagLev bombing. If you only watched the "air" version of the pilot episode, you saw this:
The problem with these screen shots is they've been CG'd half to death. The comparable screen shots from the unaired version are much more illustrative:
This one was tricky to find. Luckily there is a good clue - two of the buildings visible in the background are unique (unlike the more Vancouver-standard-modern hi-rises). You'll notice that one building has a circle with an "H" in it. It's easy enough to find when you scroll around a bird's eye view of Vancouver. I actually saw it briefly in 'Tron: Legacy' as well in a tracking shot that included the Scotiabank building.
The second building is multi-leveled and made of an unusual brown stone. I suspected it was the Vancouver Library main branch, and sure enough...
When you draw a line between these two buildings and extend it, you end up on Hamilton Street. Here are some street views of Hamilton, just north of Drake:
Note the red awning and keystone against the slate-grey building in the first street view. It's a dead ringer. Continuing to go down Hamilton confirms additional details. The exact proportions between the screen shot and the street view are a little off due to the lens used in filming, but this is the place.
In the "air" version of the pilot, the GDD briefing on the STO takes place in this building (no exterior was shown in the unedited version):
This seems to be a heavily CG'd shot with few (if any) real locations involved.
The interior of the briefing scene was filmed in the Chan center at the University of British Columbia. Both the interior and exterior of that building were used in BSG. Here's the exterior of the building (I have yet to see the interior).
After they leave the briefing, Joseph and Daniel meet up outside the aforementioned Vancouver Library.
My picture from a recent visit:
Joseph & Daniel go to a diner to smoke & drink coffee:
There are a number of clues in this scene regarding the diner's location, including the awning for Yagger's across the street, and the Ramada logo reflecting in a window (also across the street). The best clue is, of course, the "Smile Diner" neon sign in the window as shown above. This is in fact the Smile Restaurant at 424 Pender.
Neon signs & all. If you browse through the scene you'll also note that the font on "Breakfast all Day" and the other signs is the same as in the street view.
We see Joseph practicing crooked mob law:
Appropriately enough, at a room that is available for rent at the Vancouver Art Gallery, which retains much of its courthouse-era charm (this seems to be room 301):
Joseph and Sam then talk in front of the courthouse building:
which is still the Vancouver Art Gallery, in some rare interior / exterior on-site filming synergy:
Note the lions. We'll return here later.
Joseph meets William at "Wilson Elementary School", then they grab ice cream and walk around.
This entire scene was shot at the former CPR roundhouse:
Besides the fairly unique building materials, you can see the red checkerboard pattern on the ground as they exit the "school". Plus, the walkway across the former train turn-around wouldn't easily be mistaken for anything else.
Since it's hard to see from Street View or the aerial, here is the building that young William walked out of:
After school, the Adams boys head home. In the air version, you see this heavily CG'd shot of Little Tauron:
There's a lot of components to this shot, including the "Public Market" sign from the Pike Place market in Seattle:
I'm not sure how many of the background buildings are real vs. pure CG, but considering the work put into later CG shots, it wouldn't surprise me if there is no true real-world location to use as a touchstone for Little Tauron.
The unaired version of the pilot has a more realistic view outside their apartment:
Per commentary, the interior of the apartment (in the pilot) was filmed in the Waterfall building in Vancouver (as was Kara Thrace's apartment in BSG). During the series it was replaced with a set. The exterior shown above was shot at a work / live building located near 6th & Granville:
The walkways are pretty distinctive. Thanks to Alison for the tip re: this building!
We later pay a brief visit to Amanda's workplace:
I've received a tip that this building is the NRC Institute for Machinery Research at 3250 E. Mall on the UBC campus. Several scenes from Psych's Season 3 Episode 1 were filmed at this same building. However, I have yet to obtain any independent pictures of the building's interior. Here's a view of the building's exterior:
Joseph later has a chat with the Guatrau:
This was another tricky one, considering that sunken areas don't show up very well on aerials. However luck was on my side, given that the building in the first shot is very unique:
Keeping the building on your right, and eliminating other obstructions, you have a relatively small number of places where this could have been filmed. If we go down to street level at Drake & Pacific:
The building shows up relatively well. So, turning around, we see:
The curious little concrete pillars! It's a match. The north end of David Lam Park. Here's a picture from the location:
Joseph later talks to Sam:
This turned out to be easy, again using the principle of conservation of filming locations:
Remember the MagLev bombing scene? Joseph & Sam are standing under the awning on the left; the camera is pointing up and to their left, to the building across the street with the bars across the rooftop. You can see the utility poles in both pictures line up.
Joseph & Sam talk again later:
If the lion isn't a dead giveaway that they're back at the Vancouver Art Gallery, this fountain is. Look at the aerial:
Check out the pattern in the fountain. Here's a view of the fountain from ground level:
There aren't normally zombies here, but there was a slight infestation going on when I took this picture.
The last location is an interior scene, where Joseph meets with Minister Chambers:
Per the commentary track for the episode, this was filmed at SFU's downtown campus, which they described as a turn-of-the-century building. My first guess was the former department store building at Richards & W. Hastings, but reader Alison pointed out that this was likely to be at the Segal Graduate School of Business at 500 Granville. As it turns out they post floor plans online, so I suspect this is room # 1900. On a weekend trip to Vancouver I managed to take a brief look and believe this is correct. I will need to be sure to go during regular business hours sometime to take a proper look at the room.
That's it for the Pilot episode!