On a number of recent occasions, I've had discussions with new athletes regarding the differences between aerobic and anaerobic activity.  These discussions typically stem from questions such as "when will we do more cardio?" or "shouldn't we be doing longer workouts?"  In order to answer these questions, it's important to understand the difference between aerobic and anaerobic training.  Very simplistically, we should suffice it to say that the main difference between the two is simply the level of discomfort associated with whatever activity you are engaged in.  This is a mental aspect of training, which is many times the hardest part of any fitness program.  To address the physiological aspect of the difference, we must look at the metabolic pathways for energy production in the body.  I encourage you to research this topic on your own, and here's my suggested starting point:  Foundations, by Greg Glassman, founder and CEO of CrossFit. 

Here's an excerpt from the article: 

"Anaerobic activity also benefits cardiovascular function and decreases body fat.  Anaerobic activity is unique in its capacity to dramatically improve power, speed, strength, and muscle mass.  Anaerobic conditioning allows us to exert tremendous forces over a very brief time.  Perhaps the aspect of anaerobic conditioning that bears greatest consideration is that anaerobic conditioning will not adversely affect aerobic capacity!  In fact, properly structured, anaerobic activity can be used to develop a very high level of aerobic fitness without the muscle wasting consistent with high volume aerobic exercise!"

Here is a great video of Coach Glassman discussing the difference between aerobic and anaerobic training.  (You'll have to subscribe to the CrossFit Journal, but it's only the best $25 you'll ever spend on fitness literature.)

Here's an article describing the benefits of anaerobic versus aerobic training.

What does this mean to you and your workouts?

Simplistically again, your workouts must suck if you want your fitness to not suck.  This is an unfortunate situation for someone unaccustomed to suffering.  It is especially unfortunate since the suffering must be self-imposed.  Why would one endure any high levels of self-imposed suffering?  Are we martyrs?  No, we must simply understand that the long term results and benefits of suffering outweigh the temporary nature of the suffering itself.

One of my mottos is:  "workouts that suck = fitness that doesn't".  And what, exactly is meant by "suck"?  In the Marine Corps, we used to talk about the "suck factor", or the level at which something was "not fun".  If you were to hear the phrase "that was total suckage", or "the suck meter was pegged"...that would mean that that particular activity sucked and/or was filled with a much higher percentage of discomfort rather than comfort.  So, your discomfort level must rise beyond that which you are typically accustomed to.  "Get out of your comfort zone" is a familiar way to say it.

What's the bottom line?

You need to weigh the costs versus benefits.  Is the cost (heaving chest and short of breath, "cotton mouth" and searing throat pain from breathing too hard, sweat in your eyes, callouses on your hands, nausea and possible vomiting, shaky knees, "noodle legs", feelings of inadequacy) too much to ask?  Are you truly interested in general physical preparedness, the ability to confront with confidence the "unknown and unknowable" situations in life?  Would you rather tell your friends that you "went to the gym and had a great workout" while wondering if you actually accomplished anything, or would you rather say your "workout in Paul's garage really sucked", while being able to prove you did more push-ups and pull-ups and heavier overhead squats than last month?  Do you want to train in a manner perpetuated by the mainstream fitness industry and have a resulting mediocre, unbalanced fitness level, or would you prefer to use training methods used by elite athletes as advocated by CrossFit and have results that go beyond you simply feeling like you accomplished something to actually having documented results to prove it?