in reality you really shouldn't wear cuff-links without a tie/jacket combo, it just looks wrong.... pocket square is a must in a sports coat or suit jacket... if its one of those cotton jackets from the Gap it doesn't really matter and might look silly since those are not fitted.
thing is fashion is very slippery and if you're old school you prob wouldn't rock a checked shirt with a suit however it can be very formal looking depending on the accessories and combination. I prefer smaller checks to window pane or madra style.
To each his own.