Make a scrapbook with photos of the graduate from childhood till graduation and add personal notes or message next to each of the photo. This will surely surprise the graduate like no other. You can also make a photo frame with photo of the graduate along with a congratulatory note. Family photo of the graduate would just be perfect for the photo and perhaps make one of the best homemade graduation gifts.
You can also try your hand on gift baskets as they are easy to pack. All you need to do is, maybe, buy a basket, colour it or decorate it and fill with a variety of items which you think the graduate likes. Feeling them with homemade sweets, cakes and chocolates would just add to the value and touch of the gift basket.
Personalising T-shirts, mugs and frames with photo and name or initial of the graduate is also guaranteed to leave him surprise. You could also personalise them with college or graduation themes too.
The advantage of homemade graduation gifts over ordinary gifts is the touch of thought, warmth and love added to it. It is also bound to be different for the fact that it is homemade and crafted with your own hand. The recipient is also bound to appreciate more of this than any other gifts.