If you MUST fill these joints I would use a marine teak deck sealant like john2000 said. You have a serious liability issue if you have 1/2" gaps. What happens if a woman wearing high heels gets the heel stuck in there and breaks her ankle. People with bum knees and ankles will also be tripping all over the place and your lawsuits will be piling up.
You need "3m marine teak/wood seam sealer" Here is a brief description: http://www.sailingbreezes.com/Sailing_Breezes_Current/Articles/old1998/teak_sealant.htm
You can buy it here: http://www.iwol.com/boatingstore/ProdDetail/ProdDetail.asp?pid=36377&sid=2760 or at westmarine.com (or at many other places too)
If you have tounge and groove floors you are ok. If you have straight edge floor boards then I think it is best if the depth of the calking only goes down 1/2" and not the full 3/4" or 1", all the way to the subfloor. You might want to use cotton or hemp to stuff in there so your joints are 3/8"-1/2" deep. If you are going to sand the floor, which I think you should do if you haven't, then you can just fill up the joints, let the sealer harden and then sand the whole mess. If you aren't sanding then you finish your floor, then mask the edges of the seams and fill and dress the calking.
Try to get the edges of the boards as clean as possible so that the sealer will adhere well. Maybe scrape with a knife or chisle and wipe with a compatible solvent first and let dry.