On one level, this is obvious - an old school 4 x 4 league that doesn't count strikeouts will devalue starting pitchers and significantly boost closers. A league that counts hitter's strikeouts as a negative will find contact specialists like Juan Pierre and Placido Polanco in high demand. But even in more common 5 x 5 formats, there are some important factors to consider. For example, does your league require one starting catcher or two?
Most cheat sheets presume the latter, and as a result, quality backstops are given a large upgrade due to production scarcity from the position. According to Mock Draft CentralJoe Mauer is going at No. 19, Brian McCann at No. 27 and Victor Martinez at No 28. In a 14-team league, those are second-round picks.
If you were to take them based on those average draft positions (ADP), and your league only required one catcher, you'd be seriously overpaying. Let's look at what McCann's done the last two years - an average of 21 HR, 85 RBI, 63 runs, 5 SB and a .275 batting average. He might do better at age 27, but the bottom line is he wouldn't even be in the overall top-50 if he were an outfielder. Moreover, the 12th best catcher is going to get you 12-15 homers and 60-70 RBI and runs. You can see what a waste of a second-round pick McCann would be once you subtract out the replacement-value catcher numbers. Contrast that with a two-catcher league where the 24th catcher constitutes replacement value (let's give him 8-10 homers, 40-50 RBI and a .260 average), and the difference between McCann and him is stark. In that case, taking McCann at No. 27 is defensible (even if I probably wouldn't do it).
Another example is an innings-cap league. In order to prevent constant streaming of pitchers, many Yahoo! leagues, among others, will stop counting pitching stats once an owner has accumulated a certain number of innings. If the cap is fairly attainable, say 1250 IP in a mixed league, you have to assume every owner is going to get there by season's end. In which case every team will have the same number of innings pitched. What that does is turn counting categories like strikeouts and wins into averaging ones like ERA and WHIP. Instead of strikeouts, you're really dealing with K/9. As a result, you simply cannot roster Mark Buehrle, Mike Pelfrey and Dallas Braden in a 14-team or less mixed league because every inning they pitch is costing you Ks. On the flip side, Jonathan Sanchez and Clayton Kershaw get a significant bump - even if their high walk rates often keep them from going deep into games (though it does conceivably cost them some wins). A closer like Carlos Marmol who had an ungodly (and probably unsustainable) 16 K per nine innings last year was pure gold.
The upshot here is you not only have to be acutely aware of your league's rules and quirks, but you'll want to think through their implications on player value - particularly how positions and categories in your league differ from those in standard leagues upon which most cheat sheets and rankings lists are based. One shortcut you can take is by plugging your league settings into RotoWire.com's Customizable Draft Kit.