Krisis goes into
waaay more depth, but my understanding is that Deadpool's first ("Deadpool" plus "Agent X," 1997-2003), second ("Cable & Deadpool," 2004-2008) and fourth ("Deadpool," 2012-2015) ongoing series' have been omnibused in their entirety. The biggest notable gap is DP's third series, which ran for 63 issues from 2008-2012 and was written entirely(?) by Daniel Way. None of that run is in an
omnibus per se, but issues 1-12 and 50-63 were collected in OHC format.
Beyond that, of course, there's the guest appearances and two minis from 1991-1997 that, as you noted, are being collected in the Deadpool: Beginnings omnibus. There are about a billion miniseries, which have been collected in two minibuses and other OHCs ("Suicide Kings," "Wade Wilson's War," "Deadpool MAX," etc). And there was Deadpool Team-Up, which ran 17 issues from 2009-2011 and is collected in three OHCs. Plus other team books that he's been in, like Rick Remender's Uncanny X-Force.
I've probably missed some things, so anyone else, feel free to chime in. But long story short, Daniel Way's 2008-2012 series is the most notable gap in terms of omnibizing Deadpool. (I haven't read any of that series, but my understanding is that opinions are mixed.)