1.) Glue is generally sufficient. Just ordinary yellow carpenters glue is fine. Elmer's would probably work too. Clamp the surfaces together. Since two flat panels have a tendency to "creep" you could drive a screw or two, a couple of brads, or just cut them slightly oversized before gluing and then trim the finished assembled to the final size.

2.) Screws into the edge of MDF can cause it to split. There are special screws for MDF. Some require a special drill.

3.) I don't know what you mean by "color". I couldn't imagine doing anything to MDF but paint or laminate. Obviously if you want to stain it or something, any filler will never match the MDF.

Bondo would work, give the glue at least a day to dry.

Thanks a lot for your answers. Yes by color I mean paint/primer the surface so it looks all the same smoothness.

Also how should I go about sealing the MDF? Should I just use Bondo on everything or is there an easier way?

Pre-drilling is always advisable, but especially when screwing into the edges of MDF.

If you're trying to glue edge to edge you need at least some biscuits to reinforce the joint (which will align it for you at the same time).

A full length spline of 1/4" MDF would be even better. In other words, take a router with a 1/4" slotting bit and groove each piece with a 1/2" deep groove. Then rip a piece of 1/4" x 1" MDF and glue/clamp it in between. This will create a joint almost as strong as a solid sheet of material (though I can't imagine a homeowner needing to do this, unless the goal is a work surface longer than 8').

As for gluing face to face, it's best to start with slightly over sized boards, glue together, and then trim to final size, because they will creep as noted above.

Here's the trick about dealing with MDF edges...

The material is much denser on the outer skin than the inner core. So as you're happily sanding away thinking you're creating a nice smooth surface, you're really creating a "scallop effect" by removing more of the core material. This may not be apparent right away, but be prepared for a sharp intake of breath when you put any kind of paint with a sheen on it.

What you need to do is sand it reasonably smooth and then apply a coat of bondo. Don't use anything flexible like a putty knife for the purpose. Use something dead straight and rigid. Leave a thin skin of bondo, which you will later lightly sand smooth by hand.

One last thought. If water is going to be anywhere the it, see if you can get your hands on "Medex" brand MDF. You may have to visit a local cabinet shop to locate it, but the peace of mind may be worth it, depending on your application.