I finished watching Buff and Angel some time ago and loved it! I feel like it's time for more so I want to get into the comics. Particularly Buffy's Season 8 and 9 and Angel After the Fall. In what order should I start reading them? Is there a lot of crossover between the two series? What about the other ones like Spike After the Fall and Fray (I know this one is set in a very distant future, but I've heard there are some references to the mythology established there in the modes day comics).
The comics are a bit complicated because IDW developed the post-Angel storyline, and Dark Horse developed the post-Buffy storyline, and they were meant to more-or-less keep to their own characters. Angel, however, is an important part of Buffy's Season 8, and to keep the peace Willow appears in (IDW's) Spike, so there is some crossover.
In "Slay the Critics" in Buffy Season 9 #5, we're told:
I think George the fish stays at IDW. We will be pulling some of the other Angel characters into Season 9 as we proceed, but they won't always sync up with where IDW left them. Where possible, yes, but Joss ultimately has to decide where his characters are going.
So there are some continuity issues (and maybe more to come). I think this means it's reasonable to skip all the IDW's comics and go straight to Dark Horse - at top-level (i.e. Joss) canon, the Dark Horse comics are what matter, and the IDW stories are lower-level backstory canon.
If you enjoyed the Angel characters, read After the Fall first. After the Fall is essentially Angel's Season 6 - it's based on ideas from creator Brian Lynch but also plans that Whedon had for Angel if it had had a 6th TV season. If you want the ongoing story of the Angel-specific characters (Gunn, Connor, etc) then this is where you'll find them.
It's really just Angel (in a large way) and Spike (in a lesser way) that cross back over to Buffy's Season 8, and what happened to them between the end of Angel Season 5 and then isn't particularly important to the developments in Season 8, although there are references to Spike's past. We also come across Drusilla in later issues, and she's back in Angel & Faith, but we don't know enough yet to know whether the events in After the Fall are relevant or not (this might be one of those "won't always sync up" cases).
The Spike: After the Fall, Spike: The Devil You Know, Angel: Only Human (features Gunn and Illyria despite the name), and Illyria: Haunted series are really continuations/spin-offs of After the Fall, so read these after you read After the Fall, whenever that is (again, there's no real need to do this before Buffy Season 8).
Spike is the last of the IDW series, and is meant to be like what a Spike TV series would have been, rather than more Angel stories. The backstory here definitely gets pulled into Buffy Season 8 - we see Spike back in the "Last Gleaming" story and his appearance makes more sense if you're familiar with the Spike story; it's not necessary for following Season 8, though.
Read Fray. This sets up a lot of Season 8 (and beyond), and there's an explicit crossover in Season 8's "Time of Your Life" (#16-19) that doesn't make much sense if you haven't read Fray first.
Read Season 8. Nothing else is going on at the same time, so just read them in order.
Read Season 9 and Angel & Faith in publication order, i.e. swapping between them. These both start at the end of Season 8, so you need to have read those first (if you haven't read Season 8 before starting Angel & Faith, the synopsis on the first page spoils just about everything). There hasn't been much crossover so far, but there may be some coming, and the creators recommend this (from the "Slay the Critics" section of Angel & Faith #1):
Does that mean it's Angel's ninth season ...?
No - it means that Dark Horse's follow-up to our biggest series in recent years, Buffy the Vampire Slayer Season 8, consists of both the new Buffy series and Angel & Faith. We just want readers to know that while you don't have to read one title to understand the other - honestly - both series take place in the same world, facing similar challenges, in the aftermath of Season 8.
And from "Slay the Critics" in Buffy's Season 9 #1:
The groundwork for Season 9 was laid in February 2011, when Sierra, Joss, and I got together at his house with Christos Gage (who's writing the Angel & Faith book), Andrew Chambliss (who'll be writing this one with Joss), Jane Espenson, Zack Whedon, Drew Greenberg, and others to figure out how the two series would work together, with complementary directions, between these two books, and others to come over the next couple years.
The Angel and Buffy the Vampire Slayer Classic comics take place before and during both of the TV series. These are fairly standalone and while they provide a little more background, it doesn't really matter what order they are consumed in. I'd leave these until after you're well into Season 8 (since they stand alone, you can intermix them whenever you want something more) since they're not as compelling.
My suggestion would be to read them separately, either Angel or Buffy straight through. Personally I would (and did) start with Buffy. Once you're caught up with that, I'd do the same with the Angel series and then read each as they're released. There's very little cross-over between the two. I believe Spike: After the Fall fits into the Angel sequence - according to Wikipedia it falls after issues 6-8 of Angel. Wikipedia also shows the Angel/Spike/other spin-offs publishing order, which is usually the sensible order to read comics in.
Fray has a cross-over in Buffy Season 8 but you don't need to read it beforehand (I know I didn't, and while it lead to a bit of confusion the fact that you know of its existance means you're better prepared than I was).
Read them separately until Season 9, then go back & forth.