Liners
One major difference between baggies is the type of liner used.  These range from padded underwear to full eight-panel padded bike shorts with leg grippers.  Some manufacturers even make removable/detachable liners so you can "adjust" your shorts for both on- and off-bike use.  Most liners are made of mesh or a technical fabric that wicks moisture and breathes. 

A typical baggy short liner.

 

Pads
Liners typically include pads.  These are sewn into the crotch of the shorts to add a little softness, eliminate chafing, wick moisture and prevent bacteria growth.  The way that the pad is sewn into the liner varies substantially among manufacturers.  So, when looking at baggies, make sure the pad adds comfort and doesn't bunch or chafe.  If it doesn't feel comfortable, it's probably not right for your anatomy and you should try on a different pair. 

A good chamois provides protection and comfort.

 

Waistband
Waistbands vary substantially.  Most have a drawstring or belt to keep the baggy from slipping down when you're in your riding position.  You'll also find stretch Lycra panels in the backs of the shorts at the waistbands to allow the short to move with you without binding or slipping down.

Although they are highly functional, baggy shorts look like ordinary casual shorts.

Adjustability
The more technical baggies allow for a bit of adjusting in the legs, which prevents the pants from catching air or branches while you're riding.  Stretch panels in the legs or the gusseted crotch panel allow the legs to fit snugly without binding.

 

Pockets
Pocket design has a lot to do with the style of the baggy, so pick one that offers the look you prefer.  Pockets come in handy, too, for securing car keys and cash while riding.  Pocket closures include Velcro, zippers, buttons or flaps.

 

Fly
There are baggies with flies and those without.  Which is best is up to you.  A fly adds convenience for men but many riders do fine without.

Seams
Look at the sewing and construction to gauge how well the shorts will hold up to the wear and tear of regular use.  See if there are bar-tac reinforcements (horizontal stitching) at the pockets and seams that can take a lot of stress.  Make sure the seams are sewn well to take the abuse of riding through branches and brush.

Most baggy shorts come with lots of pockets for storage.

Remember that cycling shorts are made to be worn without underwear.  The pad inside the shorts fights bacteria so the shorts are actually more sanitary when worn alone. 

When you come in to try on shorts, be sure to assume the cycling position, too, so you can feel how the different baggies will fit when you're on the bike.  And when you've got them on, move around a good bit to see if they provide enough freedom of movement for your riding style.  If you have any questions at all, please let us know and we'll be glad to steer you in the right direction.