One thing I don't see this thread taking into consideration - that's important - is the fighting spirit of either party. Who's willing to go to the extremes to win and who's crazy enough to get there. You can argue the tech back and forth all day (cudos on how this thread's gone so far - these kind of threads usually get nasty fast lol) but without that information, we can't really make a good decision.
Just reading back
Cylons: have an unlimited supply of combatants until the Covies figure out to blast the resurrection ships, and that would take time. They most likely have an unlimited supply of fighters and base stars as well. It wouldn't be a case of the Cylons chasing down a rag tag fleet.. it would be full on war in the skies and the Cylons have the technological advantage AND they are tactically thinking machines. Especially if you compare them to Halo-verse humans. And, let's face it, they're just as crazy as the Covies when it comes to religion. The cylon base stars take a ton of direct damage unless a nuke is involved, and the Covies don't really have anything stealthy enough to get past the far more mobile cylon fighters. Of course, it would boil down to how the Cylons shields operated in that first battle - they would adapt, but they may lose a lot before they adapt. The Centurions would be far more of a mess to deal with for the Covenant. Not to mention the fact they've got the humanoid Cylon brains behind them... and the humanoids aren't push overs. They literally have nothing to lose because they will be resurrected.
BSG Colonials: depends on the setting. If we pitch BSG military at full strength versus a Covenant force at full strength... I dunno. It would depend on whether or not the Covies figured out how to neutralize the modern tech like the Cylons did, or forced the battle to the ground. Remember in the show, Galactica and those fighters are all old and the boat was actually about to be decommissioned. It was a flying history lesson and never meant for any further combat. The Cylons knew to win, they had to take out the newer tech, and they did so. If it's kept to the skies, the fighter force from the Battlestars are far more affective than the fighter class ships the Covenant has.
Farscape Scarrans: Their armor is pretty darn hard to get through and they are tough lizardy types to start with. I doubt slug throwers would pierce the armor and it always took a ton of in-verse fireworks to actually put a real one down. And it was always just one. Sic a whole army out and the Covies would have serious issues. Their mercs are also far more affective than the lesser armies of the Covenant. Ship wise, it's hard to compare because we didn't see a whole lot of action.
Farscape Peacekeepers: They are human, but they're also far stronger to start with. They also have basic armor, augmented armor, and they are highly skilled tacticians.. but they're narrow minded. Only problem is they're narrow minded in every skillset
except combat. Basic blaster-type weapons that come in the form of pistols, rifles, and heavy turret type weaponry. Again ship wise, it's hard to compare. It would be an assumption to say that in that world, the Peacekeepers were powerful enough to trounce everything in their way except the Scarrans - and they knew the Scarrans would be victorious in an actual war.
The Empire: I can't argue against what has already been said in here. There's two different versions of them really, in the movies and then in the EU. In the movies, they had to lose. In the EU, they're a bit more of a force to be reckoned with.. better shooting and the armor works on occassion.
The Rebellion: here's where you can't just think about the tech.. these guys would be sneaking around and may have a chance because they wouldn't fight toe to toe. Lower tech than the Empire but stealthier and they can think out of the box. In theory. Possibly.
Yahuzzan Vong: A SW race that ripped apart the New Republic and only lost because.. well it's SW and the good guys have to win eventually. They have organic technology, can go toe to toe with Jedi, strong and fast frakkers to start with, and have clamshell armor that works against blaster bolts and lightsabers. This would be a great fight to watch. They're from the same type of 'bad guy' generalization but the Vong are even more of a warrior society. And they don't have the weak points that grunts or jackals - or any species in the Covenant outside of the Elites - possess. There are different levels of warriors but they're all warriors. Since the force doesn't work on these guys though, it bears to mention that it may not work against the Covenant.
Jedi: It kinda pains me to say it, but Chief or any of the other Spartans - alone - would never get close enough to take a Jedi down. This all pends that the Force would work against someone outside the Galaxy though. The Jedi fought droids that were far more powerful than Chief. Also, if slugthrowers were actual affective weapons against Jedi... why weren't they used all the time by the Jedi's enemies? It would have had to cost less to toss a few slugthrowers at the Separatist army and say 'sick 'em'

. As far as the shields, lightsabers nail droidekas to the wall all the time. That may be one of those 'hey, we did that here but not over there" kinda things though. It definitely depends on the Jedi though - and I'm not counting anything from TFU in here. Luke at his height would massacre a number of attacking Spartans. Mace is a maybe - he relied on his lightsaber skills from what I understand so it would depend on if he's fast enough. Y'all also may be forgetting that humans in the SW world are a different genetic breed than the humans on Earth - it may very well be that they're already stronger and faster (which is suggested by how well they age) so the Spartan upgrades wouldn't have as big of an impact.
A better SW comparison would be Spartans vs Clones. I don't know how they'd exactly stack up but I imagine it would be very similiar, with the 'heavy weapons' advantage to the Spartans and the 'small weapons' advantage to the Clones. Clones are genetically bred from a Mandalorian, which at stock value are supposed to be strong warriors. Not to mention the genetic upgrades they were given. Their armor acts more like a TK's should and actually works.
I see that Serenity/Firefly was mentioned in the OP - I don't think we saw enough of what the Purple Bellies can do to really figure that one out. We know they trounced the Browncoats handily, but we don't really know how advanced the Browncoats were or weren't. We know that the core worlds are extremely advanced, but we don't really know
how advanced in comparison with other scifi. The Alliance does have massive ships as seen throughout the series and they do have a hardy ground force.
Replicators(Stargate): can't be harmed by any weapon more than once anymore.They would trounce the Covenant badly. The Spartans would have a chance because of the ballistic weapons, but would have a very narrow window of opportunity to actually defeat the replicators. They'd have to find a super weapon.
Thinking about this also brings up that Ancient device they used to destroy all Replicators everywhere - they programmed it to destroy only the Replicators. It would have destroyed all known life if they hadn't programmed it otherwise.
Ancients (Stargate): they really just have to sneeze wrong and everything dies.. so probably not fair to bring them into a tech discussion. xD
As far as Star Trek, they have the obvious tech advantage over Halo-verse in the skies with big class ships. They have a definite weakness on the ground, and didn't have a small class of fighters until the TNG movies from what I can remember, though I guess that doesn't really matter when Kirk can brag about being able to destroy easily destroy a planet. I still haven't figured out if he was just BSing in that scene though.
In closing, John Cricton would win. All he needs is his wormhole weapon and everything dies. And I mean
everything. Just spit one into the center of battle, watch it gobble up all the enemy ships who can't do a frelling thing about it, then run until it finally catches up and takes out the whole galaxy/s
Can y'all tell I'm sitting at work bored? xD