I have used the flax seed replacement in all my baked goods and never had any problem with it. I wouldn't attempt to make an angel food cake with it or anything but for regular baking I see no difference. Here is the recipe I use:
Flax Gel Egg Replacement
You'll need whole (not ground!) flax seeds, and some cheesecloth (a strainer won't work).
Quick Method:
Use 1 part seeds to 4 parts water. Simmer for 5-7 min. Proceed as described
under "Straining". For 1 egg, use 4 tsp. seeds to 1/3 cup water.
Efficient Method:
Use 1 part seeds to 12 parts water, e.g. 4 tsp. seeds per cup of water.
Soak from 1 hour to overnight, whatever is convenient for you.
Simmer for 20 min, and be sure to let gel cool before straining.
Straining
Allowing the gel to cool with the seeds in it makes it thicker. When thick and cool, pour into a bowl lined with cheesecloth. Gently squeeze out the gel, until the cloth contains only seeds. Compost the seeds, and use the gel.
To replace 1 egg, use a scant 1/4 cup gel