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
Mudd's WomenSpace 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