As far as I could remember, my local anime convention, Otafest (and previously, it's now dead winter convention, Otafest Aurora), would select a non-profit organization or charity to support.
Otafest's money goal is currently $5,000 every year (goal was less for its winter convention though), but the convention's attendees always at least double that amount! You can see how much Otafest has earned money for charity over the years on its About Us page of its website.
It may help that there are a few incentives to donate to charity, such as Otafest staff would go through embarrassment (eg. waxing their beards, get cream pies to the face, wear maid outfits, etc.) on stage at Closing Ceremonies, and other things listed below.
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To raise money for its charity of the year, there are a variety of ways to do so:
gaia_star Angel Passes are essentially VIP weekend passes, where attendees get exclusive merchandise, a con badge instead of a wristband, a free photo booth print, and to be at the front of the lines without having to wait too long. These passes are also more expensive than regular passes. The money from buying Angel Passes goes to charity.
gaia_star Cards Against Otaku is where 18+ attendees play Cards Against Humanity and have a chance to donate to charity during the panel.
gaia_star Charity Auction is where attendees bid for all kinds of merchandise and artwork. The attendees take home merchandise or artwork while the money goes to charity.
gaia_star Maid Cafe is where attendees get served yummy treats and non-alcoholic drinks by volunteer maids (and more recently, butlers as well). The money from buying a Maid Cafe ticket, treats, and drinks goes to charity.
gaia_star Sketch Drive is where attendees pay a set amount of money per character/person for drawing of their cosplay or character of choice. Attendees keep the artwork made by volunteer artists while the money goes to charity.
gaia_star Volunteer Containers is where Otafest volunteers stand at the Exhibitor Hall's entrance and have a container for attendees to put cash into for the charity. It's a good way to get rid of loose change while supporting charity!