Some good Challengers runs:
First, there's the classic Kirby run: Showcase #6-7, 11-12; CotU v1 #1-8 (1957-59). Fast-paced wonder and craziness. Wally Wood inks four beautiful issues.
Much of the early sixties stuff runs together at two and three stories per issue, but there are some standouts - a crossover with the Doom Patrol in #48, Red Ryan dies in #55 and returns in #60, and the Legion of the Weird debut in #62.
The end of the Silver Age run: CotU v1 #64-74 (1968-70) Bob Kanigher replaces Arnold Drake as writer, and from there until it goes reprint, v1 has a distinctly creepier tone. Corinna Stark debuts.
The Bronze Age revival: Super-Team Family #8-10 & CotU v1 #81-87 (1977-78): A little heavy on guest stars toward the end, but fun. Gerry Conway and early Keith Giffen.
CotU v2 #1-8 (1991): Early Loeb/Sale work is a '90s deconstruction. Essential reading, though not a personal favorite. As Kyle says, no longer canon.
CotU v3 #1-18 (1997-8): Steven Grant's Weirdoverse team is a worthy successor. The originals appear in #7-9 and in flashback in #16.
Superboy v4 #63-64 (1999): Guest appearance in the "Hyper-Tension" arc.