Watching it in the order it aired is a good idea.

http://startreklist.blogspot.com/2011/04/list-of-all-star-trek-episodes-sorted_05.html 

But, if you plan on watching the episodes through a second time when you are finished, I have a different idea.

On your first time through, when you go to watch and it is a monday (Or any day really) skip the episode you would normally watch and watch the next one instead. This way, on your second time through, you will be surprised by episodes you haven't seen.

Episodes not to skip:

**Original Series**

Mudd's Women

The Menagerie

Space Seed

I, Mudd

The Trouble with Tribbles

**The Next Generation**

Encounter at Farpoint

Hide and Q

Q Who

Deja Q

Qpid

True Q

Tapestry

All Good Things

Sins of the Father

Reunion

The Mind's Eye

Redemption

Yesterdays Enterprise

The Minds Eye

Redemption

Unification

Where No One has Gone Before

Remember Me

Journey's End

Datalore

Silicon Avatar

Coming of Age

Conspiracy

Elementary, Dear Data

Ship in a Bottle

The Price

**Deep Space 9**
Don't skip any, it is slightly more serialized, esp. in later seasons. DO NOT skip seasons 1+2 no matter what you are told

**Voyager**

State of Flux

Maneuvers

Alliances

Lifesigns

Investigations

Basics

Worst Case Scenario

Shattered

Death Wish

The Q and the Grey

Q2

Message in a Bottle

False Profits

Preemptive Strike

Hunters

Prey

The Killing Game

Flesh and Blood

Pathfinder

Life Line

Inside Man

Author, Author

**Enterprise:**

There are a lot of story arcs spread throughout the entire series, don't skip any