Just a quick GPA of the 24 teams for whom Sickels has released his top 20.
A 4
B 3
C 2

+/- = .33 (ie A- = 3.67, B+ = 3.33)

1    Rays    2.93
2    Rangers    2.80
3    Red Sox    2.78
4    A's    2.78
5    Reds    2.77
6    Braves    2.70
7    Rockies    2.68
8    Cardinals    2.65
9    Yanks    2.63
10    Pads    2.62
11    O's    2.60
12    Marlins    2.60
13    Nats    2.60
14    Dodgers    2.57
15    M's    2.56
16    Halos    2.56
17    Twins    2.55
18    Cubbies    2.52
19    Mets    2.50
20    D-Backs    2.50
21    Gnats    2.47
22    Tribe    2.47
23    Brewers    2.45
24    Royals    2.43
25    Stros    2.42
26    Phils    2.38
27    Rats    2.35
28    Tigers    2.28
29    Jays    2.28
30    ChiSox    2.28

[update] I have incorporated Sickels' grade changes, made subsequent to publishing his original lists. The difference is minimal.

~~
Cards
Gnats
Rays
Rockies
Tribe

The Rays will definitely end up as #1, knocking the A's to #5 (with #s 2-6 pretty comparable).

The Rockies could be up there too. The Giants, Cards, Jays and Tribe likely won't be.

The Rays, Red Sox and Reds have more high end talent than the Rangers, A's or Braves who have deeper systems.

Kevin Goldstein has only put out his rankings for the A's, Sox and Rangers. He seems to actually like the A's prospects quite a bit more than the Red Sox and probably the Rangers as well.
A's: 3 - 5 Stars, 3 - 4 Stars, 9 - 3 Stars
Red Sox: 2 - 5 Stars, 3 - 4 Stars, 4 - 3 Stars
Rangers: 1 - 5 Star, 5 - 4 Stars, 5+ - 3 Stars

I'd say its pretty hard to argue that the A's aren't in the top 5, overall.