One such choice concerns the accounting treatment of inventory: FIFO vs LIFO. While in the majority of cases this difference is not large enough to matter, it can make substantial differences in a handful of companies, and in the extreme case it could be the difference between a "buy" and a "don't buy"!
Consider A.M. Castle (CAS), a metals and plastics distributor. While it currently lists inventory at $232 million, it has made a conservative accounting choice (LIFO) that not many companies make; its inventory would actually be listed at $340 million were it to adopt the more prevalent FIFO method of inventory accounting.
While this may not seem like a noteworthy distinction (and in many cases, it isn't), consider how this affects the net current asset value of CAS compared to its market value:
Clearly, investors who took the time to evaluate the company's financials by digging deeper than what's on the surface could have found value that others had missed. For a discussion on A.M. Castle's suitability as a potential value investment, see this article.
Disclosure: Author has a long position in shares of CAS