Minor league baseball history is a passion of mine. The fact I just spent a perfectly fine three-day weekend writing about 10,000 words on the 1886 and 1887 seasons of Eau Claire baseball probably bears that out a bit. The sheer volume of minor league teams and players throughout the years means there are thousands of fascinating stories out there, and thousands more to be told.
My favorite minor league story is the sad-but-true tale of Steve Dalkowski. I first read about him in the early 1990's when this man who once had a lightning bolt in his arm was now scraping by working intermittantly as a field laborer whenever he was sober enough. The Hardball Times has an article here that tells Dalkowski's amazing tale. Like the article says, if you've heard of him, it's still good to be reminded of his amazing feats. If you haven't heard of him, just be prepared to be in awe of the stats and the stories. I love the attempt at timing his pitches--93.5 mph on flat ground after throwing at his maximum for 40 minutes AND following a 150+ pitch game the night before.
Don't miss the tail end of the article (after the references) for "something you may not know".