it´s nice to see people who get around to watching TOS after they have watched so much Trek already. Having grown up with TOS (and in Germany) I watched the episodes completely out of order and came to love it anyway
If you have a choice however - as you do now - I´d start with the second pilot "Where No Man Has Gone Before", as it introduces most of the regular cast. The first pilot "The Cage" was quite different overall and can be watched as a "bonus" at a later time. Plus - as has been said already - it is being re-used in the season one two-parter "The Menagerie". After "Where No Man Has Gone Before" I´d watch the next 15 to 20 episodes in production order, since quite a number of small changes took place as the series got going and it will probably be the best viewing experience when you see these changes as they actually happened. After that, especially with the beginning of season two, you can just watch them in the order presented on the DVDs/Blu-rays/online as they all stand pretty much by themselves with a lot less changes taking place.
But which ever way you´re going to watch them, I hope you´ll enjoy it