Here's a rundown on how to collect almost every single comic. List of everything you'll want to collect if you want the "complete" comic experience. It's up to you to figure out what you consider canon and what's not.
Buffy Omnibus 1, 2, 3, 4, 5, 6, 7 - Dark Horse (these are going to get you every single old Buffy comic ever printed, with the exception of one - Rogue's Gallery. The first one starts before Season 1, then jumps to Season 3, all the way up to Season 7. Not necessary canon with the new stuff, but doesn't really contradict much of the story so far. Not hardcover.)
Angel Omnibus - Dark Horse (Set in Angel Season 2 or 3. The same as the Buffy Omnibuses. Also not hardcover.)
Angel Omnibus 1, 2 - IDW (Features a random assortment of issues. Some of these are stories set after Season 5, but before After the Fall came out, so they're not canon. A couple of the stories in here are good, though. There's a few episode adaptations. Angel: Only Human is in the second one, and it's pretty important to the end of After the Fall.)
Spike Omnibus - IDW (Features some pretty important stuff for Spike. Asylum and Shadow Puppets are especially important, usually considered canon. They lead into Spike stuff that leads into Buffy Season 8, so this is something you probably want. Again, not hardcover)
Angel: After the Fall - Here's where the main canon stuff comes in. You want to collect all six volumes in Hardcover. They are: After the Fall Volume 1, First Night (Volume 2), After the Fall Volume 3, After the Fall Volume 4, Aftermath (Volume 5), Last Angel in Hell (Volume 6). The first four are considered canon, the rest aren't, but they continue the story. There's also going to be three other parts after this: Immortality for Dummies (Volume 7), The Crown Prince Syndrome (Volume
, and The Wolf, the Ram, and the Heart (Volume 9). But you don't want to buy these three individually. Instead, buy Angel: The End. It collects these three Volumes, the Angel Yearbook (exclusive comics to this edition), and the short story Eddie Hope and the Crew. This story ran in the back of each floppy issue of these volumes. Unless you want to collect it issue by issue, then this is the only place to really get it.
Angel: The John Byrne Collection - This is another hardback that fits in perfect with the After the Fall Volumes. It has some stupid stuff in it, but it has two stories that are essential to After the Fall: A Lorne short story (I guess not essential, but important), and Lorne: The Music of the Spheres. (This is essential).
Spike: The Devil You Know - Not hardcover. It has Spike teaming up with Eddie Hope for a few issues. It's not necessary to the After the Fall storyline.
Illyria: Haunted - This is a pretty important book, but it's only in trade paperback. It's discontinued, so prices are pretty high. Last time I checked, they were selling for $40. Either track the issues down individually or buy it in eBook if you're not wanting to drop the cash. I'd say it's pretty important to the story.
Spike: The Complete Series - Essential to tying everything from After the Fall to Buffy Season 8. Just in trade paperback form, as far as I know.
Fray - Another trade paperback that's extremely important to Season 8. You have to read this.
Buffy the Vampire Slayer: Tales - Collects Tales of the Slayers and Tales of the Vampires. This is a huge library edition hardcover that fits in right alongside Buffy Season 8, Season 9, and Angel & Faith Season 9. Get this. It's essential reading.
Buffy Season 8, Library Editions 1, 2, 3, 4 - Collects all of the Season 8 stuff, including the one shots. You'll have every comic from Season 8 if you buy this.
Buffy Season 9, Library Editions 1, 2, 3 - The same as Season 8. Everything is included here.
Angel & Faith Season 9, Library Editions 1, 2, 3 - The same as the others.
Spike: A Dark Place - Set in Season 7, but important to Season 10 (I guess, I haven't read it). But it comes in hardcover, that fits in right with the After the Fall stuff. Looks great.
Buffy and Angel & Faith Seasons 10
Buffy and Angel Seasons 11
The only things not collected here are: An Angel short story, which can be found as a motion comic on Dark Horse's website. There's also the Rogue's Gallery Buffy comic, which is near impossible to track down. Finally, in the Buffy: Haunted trade paperback, there's an extra two pages of Faith talking that's not in the Buffy Omnibuses. Not really worth the extra purchase, if you get the Omnibuses.
If you're wanting to collect everything, this is the best way to do it. It'll get you every comic with the least amount of crossover between books and volumes. It's pretty expensive o_O