I know this is going to sound so lame, but I love to wrap gifts. I always try to find something individual to the person the gift is for and wrap it to their tastes.
I once wrapped a gift for a friend who was into maps (yeah weird, but whatever) in an actual map of his town. He loved it. He unwrapped it so carefully so he could save the map and put it up on his wall.
Ok, so what's your Dad into? Any way to print something out and use it as wrapping? Even if you have to tape the pieces of paper together?
If you have the money a button up shirt would be funny...and then use a bow-tie as the bow. Or even use a regular tie. Heck use of the shirts and ties he already has, just sneak it out of his closet.
You could print off some pics of you and your Dad from when you were little and use the idea above. Or just use regular wrapping paper but turn it over so the white side is up, then tape the pics to the package once it's wrapped. I'm certain your Dad would love that...and probably not want to open it.
If you can get your hands on some brown paper bags (or buy some craft paper...same thing) wrap the gift in that. Then use markers, pens, paint, crayons...whatever you want or have on hand...to write nice messages or quotes on it. To make it really "manly" use twine ($0.99 at most dollar stores) as a bow, just wrap it around it like when you're mailing a package and tie it in a shoelace bow.
Depending on how big the gift is you can also make it very impressive by wrapping it in fabric. Measure the box to see how much fabric you'll need...don't forget enough to cover the end flaps...then go to a fabric store and get something rich looking. Find some matching ribbon. Most fabric stores will do up ribbon into a bow for you if you ask them...but you may have to come back and pick it up...or look on the web for how to do it...it's actually simple (maybe a friend could help if needed). Wired ribbon is best for this. This gives you almost endless possibilities. You can secure the fabric with hot glue but just be careful not to use too much and use low temp glue if possible.
Well, I'm about out of ideas for just something general for Father's Day. If I knew what your Dad was into it would help. Good luck...and you're such a thoughtful child!! :)