You've got some great ideas on here. We gave all the children bubbles at my nephew's christening, it looks really pretty but if there are very young children - usually boys - it can get a bit messy. I don't know what makes boys different but we had to watch the boys like hawks!
At my friend's daughter's christening she gave everyone ivory and silver candles which we lit during the party. The effect was stunning to have the hall lit up by 50 something candles but now that it's lighter earlier it probably wouldn't have the same impact.
You could set up a hopes and wishes jar or box where all your guests put a paper ribbon with their hopes for your daughter. You can then seal it up and when she's older give it to her so she can see all the nice things people wished for her (you may want to check through it in case there's anything inappropriate) Again it's something else your older daughter can get involved in, not only can you put a wish in the jar for her but you can also get her involved in decorating it, let her pick out beads and ribbons and help her glue them on.
I like the bible idea, if your planning to get a christening bible having your daughter pick it out would get her involved and be adorable. Also if she's a very girly little girl think about getting her a 'special' dress for the christening, maybe even let her help pick it. Even at 3 she's bound to pick up on the importance if not the significance of the christening gown so having her own nice new dress might help her feel just as special.
I hope the day is as beautiful and special as your little girls are to you.