If the Byrne FF or Stern/JRJr Spiderman omnibuses get released, they'd definitely make this list.  I have lots of favorites but if its going to just be 5 of the books on my shelf, here's are my favorites that are a bit heavier on the page count.

Until then:

1. Uncanny X-Men Omnibus Vol. 1
2. Absolute All-Star Superman
3. Legion of Super-Heroes Great Darkness Saga Deluxe
4. Complete Frank Miller Batman (Year One, Dark Knight Returns, and a standalone issue)
5. Avengers Forever


I'd like to see in hardcover:
Avengers By Perez/Byrne (181-202)
Alpha Flight by John Byrne Omnibus
Excalibur by Claremont/Davis Omnibus Vol. 1

Shazam by Don Newton