What should I use to seal the concrete floor in my basement?

First you need to determine where and how the water is entering and fix that problem first. Then the basement needs to be as dry as a bone, get humidifiers to help dry it out. Then use a good blocker like Kilz.

Sounds as if your basement needs to be "Tanked" if water is getting in.

I agree with Naomie. You need to solve the flooding problem first. Anything you put down will not survive water contact. You may need a perimeter french drain installed attached to a sump pump. Once it is solved and dry you can use Drylock to seal the walls and floor.

No sense in sealing the floor till you know why the water is coming in.

Don't seal the floor till the reason for water flooding is learned.

We did a lot of research on concrete floor sealant when we bought our office space! We wanted to get a clear sealant to bring out the natural color of the concrete. With that being said, I highly suggest using a Polyurethane rather than an epoxy, acrylic, etc. However, you will need to get the water leak figured out before applying the sealant because it needs to be completely dry and clean so the sealant lasts longer!

WE also have (or mostly had) water in our basement. We got gutters that helped a lot. However in heavy rain we still get seepage around the perimeter of the basement. It is not enough though to do the sump pump thing. But it is enough that we would not seal or paint the concrete.