Loken seemed to think that Yogg-Saron's goal was to destroy the titans ("The Pantheon shall fall," I believe he said). If that's the case, maybe Yogg wanted Algalon to send the signal in order to draw the titans into some sort of trap. Maybe he rigged the reset button to backfire on them or something.

I think it is safe to assume to that old gods are not a concept unique or native to Azoroth, a few references here and there support that they are an anti-titan faction. Whereas the Titans either create or reshape worlds for some purpose, old gods seem to infect them in a parasitic sense. The term "Seedling" used by Yogg is interesting because a seed grows into something. Perhaps if a seedling is allowed to mature you end up with something like the Naru.

Thwart the Dark Conclave - Quest - World of Warcraft

This is the only bit of in-game information that I could find to support your assertion and the quest is linked to Old Gods because the creature summoned uses C'thun's model. It could also just be a case of model recycling.

You might be right, but I don't share your degree of assurance.

I'd also be more interested in seeing how Yogg-Saron's plan incorporated Algalon, who strikes me as having the potential to serve YS like the Silver Surfer did as a herald of Galactus. Using Algalon probably wasn't even in the works, but his involvement was likely just a springboard for a future Titan raid/expansion. At least, that's where the money would be, since we've already had two Old God raids now.

There is also Harbinger Skyriss in arcatraz, whom appears to be a qiraji and when released says:
"It is a small matter to control the mind of the weak... for I bear allegiance to powers untouched by time, unmoved by fate. No force on this world or beyond harbors the strength to bend our knee... not even the mighty Legion! "

I'd guess we will have to wait for the titan expansion to see if any of these story threads pay off.

Then you will read that Mimiron explicitly say something along the lines of "Sorry friends, I was MC-ed by Yogg-Saron. Thanks for freeing me and I'll help you." You may have been too happy beating this encounter to pay attention to the dialogue, which is 100% understandable, but the dialogue is there to prove that he was influenced by Y-S.

You can also tell that he was either sarcastic and/or insane when he called you friend in that tone at the beginning of phase 1

The Quote is :
"It would appear that I made a slight miscalculation. I allowed my mind to be corrupted by that fiend in the prison! Over-riding my primary directive. All systems seem to be functional now. Clear. "

I hope that Yogg's death speech doesn't just refer to Algalon. For a long time, Metzen and co. have been building up the Old Gods as a huge threat who are subtly working the long con -- trying to manipulate events to suit their purposes over the course of many years. The corruption of the Dragon Soul, the Emerald Dream, some amount of interference in the First and Second Wars, and at least some influence and entanglement with the Lich King are all part of their C.V. I hope they follow through on that and Yogg's death actually ends up moving the plot forward in a non-obvious way.

They wouldn't even need to do that. As was pointed out by another poster, YG is the death god, so whereas it might be a stretch for other bosses, simply reducing his HP to 0 in this case doesn't seem like it should finish the job. On top of that, the last guy in the Old Kingdom does state that "they do not live, they do not die. They are outside of the cycle."

The Old Gods have very long term goals and have shown to have an influence on all manner of powerful beings - even the Lich King, by inference of the vision we see. YG had to have known that Arthas provoking the Horde and Alliance would cause them to charge blindly at Northrend, so it's not too much of a stretch to think he knew what would happen to Loken and the other Watchers once heroes of sufficient fortitude arrived in the Storm Peaks.

"Failed", or just "got killed a bit earlier than planned"?

I don't think we really know what the Old Gods are ultimately after (supposing they even have a goal and aren't just playing around), so it's probably not too safe to assume very much, especially if Blizzard is intentionally trying to muddy the waters.

Along those lines, one of the other things Skyriss says is that the qiraji "span the universe, countless as the stars". Though that's certainly a great exaggeration, why does Yogg need to build a mechanical army locally rather than just call them up?

I have a problem with the Old Gods as they're going. Unfortunately it's reasoning is "It's a game, we have to give you something to fight."

The problem is, the Old Gods have been content working behind the scenes for millennia. Now they're going all Evil Overlord and making the stupid mistakes. Send the weak minions out first, then the strong ones, then deal with it themselves. Announcing themselves and their grand plans publicly before the plans are complete. And so on.

If these things were vastly powerful and devious then by all rights we shouldn't know they're present until they've already achieved their goal. 2 out of 2 Old Gods going "Wow, finally out of jail, I'm so happy I'm gonna shout my presence to the world" is at least 1 too many. They should have let Brann in, let him talk to the Titan computers, and when he walked out he'd say in a monotone "Everythin's fine in thar. Ignore Ulduar."

Attacking people the instant they enter Ulduar is just foolish. They're not behaving like grand schemers, they're behaving like a newborn who simply reacts when you poke it. If they can wait thousands of years, why are they all knee-jerk reaction when people show up? Play dead, pretend nothing's changed, whatever. Heck, have General Vezax plaster over the door to your room and paint it like a wall - no one would know something is even missing.

In short Y-S has no motivation to act as abruptly and foolishly as he has. I could forgive C'thun as outright war almost worked last time so he just tried it again. Y-S knows better, but is entirely breaking character.

I'd assume that being still partially trapped within a titan prison would have ones influence and ability to communicate at a little less then intergalactic.