I will only mention the most obvious one, but we may add some later.
OLD TESTAMENT MIRACLES
Burning bush
May have been acacia plants, which are known for making great charcoal. Mount Sinai has been claimed to be a former active volcano. It could be argued that a volcanic vent lit up acacia plants and that would be the origin of the burning bush. Benny Shannon argues that this could be combined with entheogen plants such as Peganum harmala and acacia tree in the vicinity of Mt. Sinai thus attributing the divine revelation to an psychedelic experience.
Turning a rod into a snake
This is a magic trick.The two ends of a snake, the tail and mouth-end, are held in two hands and the reptile pulled straight. Strong pressure in the centre of the head with the thumb and the pointing finger held on both sides makes the snake stiff. It cannot move even after lowering the tail-end to the floor. It looks like a rod. To make it crawl again let free the hand gripping the tail part and shake the snake and throw it on the ground; within a few minutes it will regain its moving power and crawl away.. This is why the egyptian wizards could perform it too.
Challenge to Baal
Elijah and the Baal followers competed to see which god was true. They took a bull and decided that the god that could set it on fire was the true one. Notice that Elijah commands people to pour water on the body and shortly it ignites. This could be achieved by introducing sodium crystal which explode when in contact with water. The same effect could be achieved by pouring glycerin on potassium permanganate hidden within the sacrificial animal, passing it as water. Naturally occurring lithium is an a more likely explanation given that potassium permanganate and sodium could not be obtained during that time. My bad.
NEW TESTAMENT MIRACLES
Turning water into wine
Keep in mind that they were asked to pour water on already prepared jars (John 2). It could be possible that these vessels could be trick vessels, like in here. Jesus is not the only religious figure to turn water into something else. Shirdi Ke Sai Baba turned water into oil although this could be achieved by pouring water in vessel that already contained oil thus bringing it to the surface. In some cases, a transparent substance turning wine-coloured could be used
Walking on water
This could be achieved by a variety of methods. One could build a secret platform or take advantage of a naturally occurring one use cornstarch to create a non-newtonian fluid which behave like solids under pressure to have people walk on it (like the Mythbusters did) or it could be simply an optical illusion.
Healings and exorcisms:
Back then, medical knowledge was practically non-existent and was mostly folklore-based (Leviticus 14). The method of putting a mirror under the see if it fogs up is widely known and regarded as not useful. The lazarus syndrome is also known. Premature burials are pop culture. My point is that mistaking someone alive for dead was pretty common back then, as it was in even posterior centuries. Blindnesses could be hysteria, pains could be alleviated by placebo effect, like faith healers do nowadays.
Demonic possession was employed to explain a wide arrange of mental illnesses as well as rabies, epilepsy, tourette syndrome, etc. An exorcism could serve as psychological tool to diminish symptoms by placebo or psychologically. Usually exorcisms take many sessions because the symptoms keep coming back; consistent with mental illness.
Multiplication of food
Explained though could be explained by gross exaggeration.
MODERN MIRACLES
Holy Fire: Considered a fraud and exposed on TV
Holy Snakes: The snakes that appear at Kefalonia are usually docile and their fangs are at the back of their mouths, so they aren't a threat to humans. Their appearance could be attributed to mating rituals.
Miracle of the sun: Staring at the sun causes pupils to contract thus dimming the sun, retinal bleaching explains changing colours and the people looking purple/yellow (Opposite colours; What a coincidence!). There are cases of documented retinopathies like at Knock.
Weeping statues: Putting fluids inside a hollow statue and scratching the eyes could cause the liquid to pour out as if it were crying blood, oil, or water.
Levitating saints: St. Teresa was poorly documented. St. Joseph of Cupertino baked rye bread which could harbour hallucinogenic fungi.
Incorruptibles: Most bodies are corrupted, some wear wax or silicone masks. None of them are miraculously preserved.
Saint Januarius: Not actually blood but a chemical compound that liquefies with heat and mechanical stress.
Eucharistic miracles: Serratia marcescens, fraud, pareidolia.
Rosaries turning into gold: Some metals turn golden when oxidized.