The first 20 issues are "setup". Good issues, establish the universe and characters, but clearly they were finding their legs.
21-30 really introduce a new big wave of '84 characters and set the stage for the best run. The silent issue and origin of SE
are awesome. 31-57 + YB3
are what I consider the golden age of the Marvel run. It's some of my favorite comics of all time, Joe or otherwise. Mostly penciled by Rod Whigham, these stories stand the test of time and are a blast to reread.
58-78 are very good. The whole gulag saga and the cobra civil war are great, but you can feel the less popular elements creeping in, such as BF2000.
79-99 was a somewhat stagnant era, sort of a holding pattern as the comic tries to decide what direction to head. More ninjas and sci-fi elements creeping in. Overall, some good stuff, but not what I consider the best.
100-118 the comic gets a second wind, and there is some pretty neat stuff in there. The whole middle eastern war and the deaths of many long time popular Joes really crank the action knob to '11'.
119-154 are a very mixed bag. There are some neat stories scattered amongst some real crap. Ninja Force, Eco Warriors, Transformers Generation 2, and other goofy elements really hit home that the toy line was throwing ideas at the wall to see what would stick (not much did), and the comic was forced to follow along. :(
155 - Who wouldn't love this issue. Great stuff.