2) Photo - carry a picture of your loved one with you during the day. I've seen some lovely ideas of a photo collage or a table with framed photos of your loved ones who've passed away, but, those didn't speak to me as much as physically carrying a photo with you. This is an easy DIY that you can do together, creating a very special memory as you both share stories about your loved ones. Once you've made your charms, you can add them to your bouquet, boutonniere, necklace, whatever speaks to you.
3) Clothing - there are so many ways to use a loved one's clothing in your wedding day. Wear their wedding dress/suit, if you can (and the style works for you). Carry their handkerchief in your hand, or tucked into a pocket. If you, or someone you know, sews, make your garter out of a piece of your loved one's clothing; this idea works for a groom, as well, instead of a garter, make it into an arm-band. Cut out a piece of their clothing in the shape of a heart and have it sewn into your dress/suit. There really is no limit to what you could do with this idea.
4) Food - add a favorite food of your loved one's to the menu. Thinking about ways to use food to honor a loved one brought an interesting idea to mind. With the popularity of dessert/candy/popcorn/you-name-it bars at wedding receptions, why not have a cookie bar? All of the cookies could be made from your loved one's best cookie recipe, and put signs in front of each plate of who's recipe it was, and why it's special to you. I think this would be a fun way to honor several loved one's at once.
5) Donations - I absolutely love the idea of a donation to charity in honor of a deceased loved one! Instead of getting wedding favors for your guests, you can choose a charity that was special to them, or one that supports a cure for the disease they died from, there are so many to choose from. Put a sign on the guestbook table that says which charity the donation is going to, and who it's in memory of. Add a small collection box so your guests can donate to the charity as well. Personally, I can't think of a better way to honor a loved one, than helping others in their name.
When it comes right down to it, there is no right or wrong way to honor someone who's no longer with us. It's what speaks to you as the best way to remember them.