In my experience, the one thing that makes a wedding unique is to put a little of yourself and your fiance into every detail. This is not only true of my own wedding, but every wedding I have gone to in the past. I always remember the weddings of those people who clearly put a lot of time - not money - into everything.
For example, my table names were a few layers of simple 5x7 cardstock that we printed on our laser printer ourselves. We did not spend a lot of money on them, but we did spend a lot of time on them. Pete (my DH) and I wrote little stories about our relationship and the title of the table was a key word from the story. Instead of "Table 1" and "Table 2", we had "Engagement" (how we got engaged) and "Ireland" (about our driving trip through Ireland). People were walking around from table to table to read them all, and that led to people mingling and having a better time.
We tried to put a personal spin on every detail. On each of the girls' bouquets was a (cheap) rhinestone pin with their first initial. We put together a CD of significant songs to not only me and Pete, but included the songs from our dances with our parents, etc. I made the invitations, programs, etc. etc. While they looked rather professional, we saved so much money on the programs that we could include extra pages. One page had an entire paragraph devoted to thanking our guests. We wrote our own vows and also included those in the program.
We got so many compliments after the wedding. They weren't about the food or the flowers or even the location. They were about how much the guests appreciated all the effort we'd put into making them feel like a part of our relationship, and therefore how special they felt to be a part of the celebration of our relationship.
I have more examples, but the point is that you sit down and try to make every detail (big or small) about you and your fiance, as well as your guests. That means we, here on the board, might not be able to tell you how to make your wedding special - since we don't actually know you. But once you come up with some ideas, the girls here could definitely improve upon them and help you make them better.
I'm a firm believer: a unique wedding is a personalized one.