I've always felt that a truly great relationship between God and humanity would entail no miracles, for such reasons as how the Babel Fish disproves his existence. For faith to be true faith, God should have no palpable mark upon the world. The thing is, in becoming a devout Catholic I've encountered a great deal of phenomenon that speak to the contrary; God has left an indelible mark upon the world that is there to be observed by anyone paying attention. This is of special interest to my theory of Metaphysical Consequence because it rules out the initial picture it paints of an essentially deist world.
Probably my favourite miracle is that of Lanciano, which I have seen personally. It has undergone rigorous scientific scrutiny, against which I have never encountered any viable explanation for it. Furthermore, it gives plausibility to the authenticity of the Shroud of Turin. Not only do the blood types match (both are AB), but I've heard somewhere that the DNA is a match. When I looked at it, it really did seem to change colors before my eyes. Read about it here:
http://www.therealpresence.org/eucha.../lanciano.html .
Another favourite is that of St. Francis' rosebush, for which the only online documents I can find are travel promos. Basically, St. Francis of Assisi was overtaken by guilt for a mental temptation. He decided he had better punish himself, so he sprinted towards a particularly thorny rosebush and leaped onto it. When he landed on it, all the thorns disappeared. Not only is an offshoot of this bush still there (I've seen it), but recently botonists strived to classify it. Their conclusion was that it's an entirely new species of rose (not just a hybrid), to which it is the world's only specimen.
Another one I like is the Sun Miracle of Fatima, particularly because it was so widely documented at the time it happened. It was first reported by a Portugese state newspaper in 1917, which would naturally be antitheist in nature. Read about it here:
http://www.fatima.org/miracle.html
Another one which is remarkably unheard of is the story behind the very well-known image of Our Lady of Guadalupe. A synopsis is here:
http://www.cancunsteve.com/guadalupe.htm . But what that doesn't tell you from what I've seen is that the cloak on which the image appeared was made of cactus fibers deteriorate within forty years on account of exposure to oxygen, yet has lasted for more than four centuries. Furthermore, it doesn't really point out the obvious fact that these roses were picked five whole months out of season for them to be blooming, and they were actually Castillian roses not native to Mexico.
Anyone else have favourite miracles?