Often, I hear people spouting the cliche, "God works in mysterious ways." It's raises an eyebrow for me as people use it during the darnedest times - like when they don't win the lotto, or their plan for the church gets rejected by the top brass. Or when they get a gut feeling that they avoid riding a certain bus, then they learn that the bus had an accident later. Yes, sometimes God's ways seem mysterious to people.
However, the saying does not come from the Bible. It comes from a poem written by William Cowper in the 18th century. His poem may be inspired indeed. But the poem's title and first lines have been among the most cliched and misused religious slogans of all time. In addition, people may quote it as a Bible saying. They should be careful of that. It is not in the Bible.
There are of course some sayings not in the Bible that are still in line with Christian belief. Among the ones I prefer are "Cleanliness is next to godliness," "Nasa Diyos ang awa, nasa tao ang gawa (with God is mercy, with people is action)," and "God helps those who help themselves." I prefer those sayings that remind people of their own responsibility to act, and never like one should pray to God and wait for manna to fall the next day. "Let go and let God" for example has its applications at times, but I believe it is a very misused slogan.
I'd rather not overuse sayings or use them out of context. But on "God works in mysterious ways," I believe that if you really know God, he or his ways won't be mysterious to you. It's only mysterious to you when you don't agree with his ways or don't get it. Basically, human pride gets in the way, you don't get it, and feel that God's way is mysterious to you. But if you get it, you won't think that God works in a mysterious way again. It's just that he works for your own good.