Get 100 rupees quickly each time you start playing.  After you get the Blast Mask, go through the Bomber's secret hideout.  When you get into the sewers area, go left instead of right.  You will find a ledge there with a bombable wall.  Inside is 100 rupees.

Also, after receiving the bunny hood, go onto the roof of the bar and jump off.  You should land on a ledge above the exitway.  Jump again onto the basket above the lover's place.  Jump over to the next ledge, climb up, go around the archery game, and you will find another chest with 100 rupees.

A simple and effective way to kill enemies as a Deku Shrub is to hide in a flower.  Wait until the enemy is on top of the flower and then pop out.  This is especially useful against the turtles.

Make sure you wear the Great Fairy Mask in every room in a temple.  Even the plainest rooms sometimes hide one.  If you can't find it, try using the Lens of Truth.

If you are having trouble beating a temple in the time limit, try beating it in three stages.  First get the item, map, and compass.  Then go back and beat it in the next 3 day period.  Finally, go back and search for the fairies.  This is only if it's a long and difficult temple, of course.

If you are having trouble with the UFOs, slow down time.  They will move slower as well.  And don't use Epona.  Remember the ones in the back too.

Wear the Mask of Truth and enter the dog racing area.  Then pick up some dogs to see which ones feel confident.  You have a better chance of winning that way.

If the bird in Hyrule Field steals your bottle or sword or whatever, you can get it back at the curiosity shop. 

Play the lottery for each day.  Write down the numbers.  They don't change when you go back in time.  

In the second skulltula house (and maybe the first, too), there are skulltulas living in the jars.  If there is no lid on the jar, it's in there.  Get on top and do the Goron stomp.

Also with skulltulas, to get the ones in the tree or on the chandelier, just turn into a Goron and do your stomp move.  They will fly out.

If you are looking for the frogs, there is one in Woodfall on a log and one in the laundry pool of Clock Town.  Also, the Gekkos in Woodfall and Great Bay Temples turn into frogs.