Most here will tell you to use Dow795. I've used lexel with huge success. Kind of messy.
There's much to like about butyl tape for bedding deck hardware. It takes a bit longer to apply, but it's easy, relatively mess-free, and the job is finished as soon as the nuts are tightened - no waiting for the sealant to cure. It's the best choice for framed portlights, but should be avoided where it may come into contact with chemicals. It does not cure, so butyl tape properly installed should remain watertight for decades, yet it's also the easiest to dismantle.
If you can't find butyl tape or have more faith in a curing sealant, Boatlife Life-Calk polysulfide, applied as described in the article, "Re-Bedding Deck Fittings", will be your best choice for bedding metal and wood (but not ABS or Lexan) because of its excellent chemical resistance and emphasis on sealing rather than bonding. The polyethers accommodate movement better than the polysulfides and have better UV resistance, and 3M 4000 UV is even compatible with plastic. But the stronger bond will be problematic if disassembly is required.
Sikaflex 295 UV polyurethane is another alternative to polysulfide. A combination of superior UV resistance, liberal elongation, and compatibility with plastic (in concert with a primer) makes this a versatile sealant. Its advantage over 3M 4000 UV and over all of the other polyurethane products is its lower strength, which makes future disassembly/removal easier. You can, of course, use any of the other polyurethanes, but unless your intent is to bond rather than seal, these are choices you may come to regret.
The alternative for sealing framed windows, if you skip butyl tape, is silicone sealant. Bonded windows require a structural glazing silicone such as Dow 795 (or Sikaflex 295 UV polyurethane protected with a special primer). Beyond portlights and specialized uses, you'll save yourself grief if you keep silicone sealant away from the deck and hull.
Don't just pick up any tube of marine sealant from your favorite chandlery and set to work. If you want to make sure that leak doesn't come back, take the time to select the best sealant for the job. While it may not be as much fun as playing with drills and bolts, choosing the right sealant is every bit as important as the proper technique to make that fitting watertight.