[quote name='Tronny']In order of both time-wise and quality-wise: Civil War > House of M > Secret Invasion.[/QUOTE]
Isn't it more like, chronologically: Avengers Disassembled (2004) [since this kicked off the current age of mega events] > House of M/Decimation (2005-2006) > Civil War/The Initiative (2006-2008) > Secret Invasion/Dark Reign (2008-2009) > Siege/Heroic Age (2010-2011) > Fear Itself/Shattered Heroes (2011-2012) > up to Avengers vs. X-Men (2012), which will undoubtedly have a tie in aftermath event.
I think those are pretty much the big events Marvel pushed for those years. Of course you have other "events" in smaller corners of the universe, like all of the Hulk events, Cosmic events, X-Men events smaller in promotion than House of M (but have big effects on the X-Men corner of the Marvel U), Spider-Man events, Doomwar, hell, even a street-level event with Daredevil's Shadowland.
And yes, Waid's Daredevil might be the most critically acclaimed Marvel "cape and tights" book at the moment. Rucka's Punisher also gets much critical acclaim.
As far as Omnibus vs. Ultimate Collection, Omnibuses are oversized hardcovers. Oversized as in the paper and stuff is bigger than your standard comic book. As far as Astonishing X-Men goes, the Omnibus collects all of Whedon's run on Astonishing X-Men in one oversized hardcover. The Ultimate Collections collect the same issues, just in two volumes instead of one. So it depends what you want out of your trade experience. Are you looking to collect and display books? Are you really into seeing artwork in a larger format? Then get the Omnibus. If you're just going to read it and not care about the collecting aspect, jut get the paperback Ultimate Collections. But I wouldn't recommend Whedon's Astonishing X-Men unless you already hardcore love the X-Men. I think it's massively over-rated since some of his stories are just downright silly even from a "this is a comic book world" standpoint.