If you can draw (even a little bit) you could make a cartoon of the 2 of you and then come up with some sort of funny/sweet caption to go along with it.
If you can’t draw, try to find a comic in the funny papers or in a magazine that just seems “perfect” for your situation.
If there is a chain restaurant or coffe place (like Starbucks) where you guys went together, at least once, get an inexpensive gift card (enough for one sandwich, or one burger and a coke, or one fancy coffee drink) and enclose that in your package. Tell him that you will be going to the same place (in your town) on such and such a date at such and such a time and that you will be enjoying a snack “together at the same time in the same place and thinking about being together, although you can’t be there physically.”
If you know he loves a particular outfit that you have, put it on and have one of your friends take a photo of you wearing that outfit holding a little sign that says “me missing you.”
Find out from his mother what his favorite cookies were from childhood (that she used to make) then have her give you a copy of the recipe, in her own handwriting, then you will make those exact cookies and send along the recipe to him.
If you can get a childhood photo of him (from his mother) then find a photo of you from approximately the same age and put the 2 pictures into one of those little double frames.
Make a cute little coupon book for him “to redeem at his leisure” with things like: one free kiss, one free neck massage, one free batch of home made cookies, one free walk in the park, one free load of laundry, one free whisper of sweet nothings, one free home cooked meal etc.
This one will take a little planning on your part, but Target and other stores will make a custom calendar for you. Put together a calendar for 2012 and have a picture of you made for each of the 12 months. Maybe one of your friends can help you by taking the pictures and finding appropriate outfits and settings. It might be a little bit difficult to figure out what to do for the December picture, but be creative, figure it out. Do you live anywhere near any pine trees? Put on a hat and gloves and a scarf, get some fake snow (or bust out your Christmas decorations). Just make sure all of the pictures really represent each of the months.
Do you wear any particular perfume or use any particular type of fabric softener that he likes the scent of? If so, put in a little piece of fabric with your perfume or other scent that you use that he likes. I was just remembering this funny episode of The Nanny, where Niles the Butler sprayed some Lemon Pledge on a piece of fabric for C.C. his soon to be wife.
You could make an outline of your hand on paper, then cut it out and put that in the package so that he can “hold your hand” any time he wants to, until you meet again. You might also want to make a lipstick kiss print, for the same reason.
Pick a date and time (either a random date, or one that has significance to you both) and tell him to go outside and look up at the moon on that date and time and make a wish. You will be doing the same thing at the same time. Maybe enclose a glow in the dark moon (that you can get at Target or Walmart in the toy dept.)