Mostly reposts from elsewhere for the moment.
* What actually became of Haller? Tycho says on "Hairy Legs" that the ship that Durandal had you send Haller to, the UESC Triumph, doesn't exist, and you in fact helped Durandal do a bad thing. However--remember the seventh terminal back on "Honk if You're an Underpaid Cyborg"? The one with the line "Send_To: Tactical Analysis, UESC Triumph"?
Pretty sure Tycho's the liar here. Durandal's pretty serious about the UESC-Pfhor war effort as long as he doesn't know that Tycho's still alive, so I doubt he'd compromise it by not giving Haller back (he did probably have Haller's escape pod momentarily dock at the Rozinante for architectural analysis and note-taking, though). Plus, as far as I can tell, there are no real signs that Durandal assimilated what remained of Haller.
* Poking around "10001 Nordic Nerds", you can find a terminal claiming that Arthur Frane hand-coded the RNA structure of the Achilles virus; however, that was actually Lysander's doing. Obviously a bit of misdirection on the Dangi Corp's part, but does it hold any significance beyond that?
There could be any number of explanations for that; the one my brain jumped to was "Frane was Lysander's creator and possible overseer like Strauss was to Durandal, and thus the guy who'd have the easiest time successfully misleading the UESC should they suspect something".
* Around the midway point of "Frog Blasting/Blasted Frogs", Durandal discusses the remains of organic Jjaro AIs that he came across while the Security Officer was in stasis, and suddenly says, “You can imagine how wastefully constrained I must feel here, dealing with old threats improperly handled in the past, reopening ancient wounds that should have been healed and forgotten ages ago.”
The old Volunteers series assumed he was talking about his own possible mortality, IIRC, but I think this was actually an allusion to Tycho, with whom Durandal clearly has serious issues. He didn't handle Tycho properly in M2 (leading to Durandal's capture and presumably month-long torture), and the sight of him must've brought all those unpleasant memories right back to the forefront.
In addition, Durandal's more jerkass-y than usual on this level (meta-wise, because these terminals were the sole writing contribution of one team member), so perhaps his frustration over Tycho is mounting.
* Speaking of Tycho, "It's not my brain..." is a weird level story-wise. You're sent into what I assume is the Pfhoric boonies to retrieve the one clone of his that he hasn't already re-assimilated...but this 'clone' seems to be the Tycho from the UESC Marathon, who remembers you as Durandal's errand boy.
Seems to be; my guess is, that's a clone that happened to retain Tycho's memories of his time there. The original Tycho does specify that that was the data he copied; plus, his earlier use of the term "re-assimilated" on "Carpe *mumble mumble Latin*" does sound a bit like all those copies were carrying fragments of his mind, or something.
Plus, Tycho not being the original would undercut his eventual victories over Durandal in two of four Planks, so.
Any further theorizing would be welcome, especially on stuff like whose dreams the SO was actually experiencing and if "Dangi" actually means something (some kind of Norwegian wordplay I'm not getting?).