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The most common wood species for dowel rods is birch for most utility type work, but you can get walnut, oak or other types of wood generally found in furniture and cabinet work.
Dowel rods come in sizes from a very skinny 1/16 inch diameter to larger sizes up to three and four inches in diameter. Common lengths are 36 inch and 48 inches long, but the larger diameters can be found easily in lengths up to eight and twelve feet long. The longer large diameter dowel rods are more commonly called closet rod or handrail.
Dowel Pins
Dowel pins come in assorted sizes too. They generally range in length from one inch to two inches and in diameter from 1/4 inch to 1/2 inch. Other sizes can probably be found too for specialized applications.
Dowel pins generally have the edges knocked down on the ends to make a rounded end to make them easier to get into the hole drilled for them.
 Dowel pins have two methods to let air and excess glue escape from the dowel hole. Some dowel pins are fluted, little grooves the length of the dowel pin all around the circumference and others have spiral dowel pin grooves all around them. If they weren't grooved to release air and glue from the hole the air and glue would compress and would make a weak joint that would expand as soon as the joint was left on it's own. 
The dowel hole should be just slightly deeper than the length of the dowel to go into it to help alleviate compression of the air and glue in the dowel hole.
Dowel Pin Grooving Tool
Periodically we'd run out of a size of dowel pin and have to make our own, so I made a grooving tool. I took several scraps of 1 x 4 and drilled dowel pin size holes in them, one for each diameter size dowel pin, then drove nails in so the points were just sticking through the holes. I put the grooving tool in a vise and took a few inches of dowel rod and pounded them through the hole with a mallet and cut them to length. Amost instant dowel pins.
Doweling Jig
A doweling jig is a must if you're going to join boards edge to edge. The dowel hole center needs to be a precise distance from the top of the board on both boards to be joined so the boards can be as smooth and even as possible along the top surface.
 The Dowel Pro Jig is a handy tool, because you can clamp up both boards at the same time and the guide holes in the jig are set to drill precisely in each board to get an exact fit.
If you have several boards to join it's very simple to remove one board and add another to drill the dowel holes exactly from the top surface of the board and from the ends of the board.
 The Self Centering Doweling Jig is great for thick timbers and opens up to a full six inches. It can be used on narrower stock too. As you clamp the doweling jig onto a timber the drill guide in the middle centers itself exactly so you get the dowel holes centered on each timber to give a pretty smooth top surface after the timbers are all joined.
No matter how precise the holes are you will always have some sanding to do to get a perfect surface.
Dowel Center
 A Dowel Center is for those times that it wouldn't be possible to use a doweling jig for various reasons, such as adding a board to a built in surface. The dowel center is made of metal and comes in various sizes to fit in dowel holes of common sizes. The dowel center is very precisely sized to fit exactly in a dowel hole and it has a point on the side sticking out of the hole sticking exactly out of the center.
Dowel centers are inserted into predrilled holes in a board to be added, then the board is moved so the points of the dowel centers are exactly where the board is to be added. The board is given a healthy tap on the opposite edge from the dowel centers using a rubber mallet to keep from denting the board. The point on the dowel center will leave a little dimple for a starting position for a dowel hole.
Wood Plugs
There will be times that you can't make a blind dowel joint or that you need to drill a hole for a screw and you need something to fill the hole. There are several different kinds of wood plugs available.
 A Screw Hole Button is a mushroom shaped plug with a precise fit for the hole with a rounded overlapped top which leaves a little bump where the screw hole or dowel hole is.
 Another Wood Plug is tapered on it's sides and taps down so there is a slight rounded bump where it is. Another wood plug is tapered and has a flat top that can be sanded down to be exactly smooth with the surrounding surface.
Dowels
Use dowels wherever you can when you're joining things together they'll make the fit more precise and will make the joint many times stronger than a joint without a dowel pin helping to hold it together.
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