I'd have to put McFarland, USA as the best running narrative movie ever. I'd still rank Without Limits in my top five, simply for how well it effectively conveys the intended vibes at many points in the story (his freshman year experience, interactions with Bowerman, post olympic season). I find faults with how Without Limits tries to be inspirational at points (which I don't get how a character with unattainable talent can be particularly inspirational to the common viewer) while the narrative is undermined by questionable acting. McFarland, USA does a great job in speaking to both younger and adult audiences effectively, while I find that Without Limits doesn't in this aspect. Some scenes in Without Limits seem intended for a very small segment of the audience and will leave the rest either rolling their eyes or not understanding it. Without Limits might work best for the 16-17 year old male (I was 17 when it was released, so my higher ranking of it might just be for nostalgia), while McFarland works better for every other demographic.
Tier 1 (I'd put in my personal movie collection):
McFarland, USA
100 Seconds to Beat the World
Tier 1 Honorable mentions (not really running movies, but has a running scene, is about a runner, or at least captures the spirit of running training at points): Breaking Away, Icarus, Gattaca, Chungking Express (has my single favorite running scene ever), Rocky, The Graduate
Tier 2 (I'd re-watch for one reason or another):
I Am Bolt
Without Limits
Chariots of Fire
Tier 2 Honorable Mentions: 14 Peaks, Forrest Gump, Rocky IV
Tier 3 (liked these, but I'm not interested in seeing again):
Saint Ralph - this is by far the most misunderstood running movie. Panned for its unrealistic conclusion, being unrealistic was the exact purpose to drive home the main theme.
Prefontaine (I actually find this one more interesting than Without Limits, but Leto ruins it for me)
Marathon Man - great running/training scenes. Inferior narrative to other films of its style of it's time.
The Loneliness of the Long Distance Runner (this might be the best running movie ever, if judged purely from a non-runner critics perspective) One really has to be in the right mood to watch this movie, and I rarely am.
Tier 3 Honorable Mentions: Race to the Summit, Hustle (great hill interval scenes!), Unbroken
Dishonorable mentions: I've seen LOTS of running documentaries that I simply don't like - though I admit it's likely because I already know the stories and don't find them worth watching for the information I'm getting out of them.