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It's great that you want to honor your friend---the key is to keep it classy and not to depress your guests but do it it a manner of celebrating her life. You have several options. You can write a tribute/poem to your friend in your program, have a moment of silence in the ceremony to honor her, light a candle in her memory, play one of her favorite songs during the ceremony or toast her at the reception.
A wedding isn't really the best place to be collecting money for a charity; couples aren't even supposed to ask for gifts in any form, so coming right out and asking for donations could be construed by some guests as tacky, no matter how good your intentions. You could spread the news via word of mouth that you'd like donations to be made to the American Cancer Society in lieu of gifts, or you could donate monetary gifts from your wedding to the organization in her name.
When I got married at 41 years of age, I had a flower girl for every close family member not there .. such as My mother and My grandmothers.
IT was lovely and they looked like little angels. NO WINGS just flowers in their hair and baskets of flowers wearing matching dresses in different colors of the wedding theme.