Glad you're enjoying the trip, Kattoelox!
Regarding SSM, put me in the camp that loves it from start to finish. To me, Operation: Mindcrime's weakest full song is ironically the title track. But "weakest" is not really the right descriptor, because I still very much like it. That whole record is pure musical perfection to me.
"Anybody Listening?" is my favorite song from Queensr˙che. It encapsulates everything great about the band in a six-minute or so (not counting the outro, which is cool in its own right) tune. It's like they took the mid-tempo dramatic vibe from "The Mission," let it breathe a bit more, and Geoff wrote lyrics that could connect with pretty much anyone, even if it was written from his perspective as a performer. The whole song is incredible, and really, at least for me, the pinnacle of the band's songwriting abilities.
"Open Road" from the TLT-era self-titled album goes for that vibe and captures it a bit. But like most, I think the song is under cooked. Wish they would have had more time to flesh it out a bit more.
The description bosk1 gave of "Empire" is spot-on, in my opinion. I loved it from the start. I remember seeing that video and hearing the song for the first time. I loved it immediately. It didn't even dawn on me back then that they had gone more "commercial" or "polished." It was still the dark Queensryche, and them doing a song about the drug wars and conflict. All the heady stuff I expected from them.
I didn't hear any other tunes from the Empire album until I got the CD at Christmas that year. Once I did, I did notice it wasn't as "metal" as the back catalog, and more hard rock, but I never really gave it much thought because it was so damn good. Plus, most bands were doing the same thing in the early 1990s, so it just seemed (and still does) a natural progression for Queensryche.