Well I belive the best order to watch it, is in fact the order that the Anime was presented to us; or in other words... "as aired on T.V.".
This was actualy a very smart way to deliver the story content, but of course it would not have worked if Haruhi's caracteristics as a character had served as an influence to do such.
The development of the series storywise can be very well acompanied through its correct order yes.., however, and this of course.. giving its content, on the way the episodes where switched it actualy ended up emphasizing some in climax sort of prespective.
For as we know.., the last episodes of Haruhi (as shown in "as aired on T.V.") are actualy some of the first episodes to storywise.. be aired.
However.., these are the episodes that give us the conclusion to what the Anime is all about, and what realy are the facts & explinations behind some of the events we first got to see.
Hence, this way, they where able to deliver us something "unique" when watching it.., not only it felt as if miss Haruhi was realy in charge and much like
NoSanninWa said & I quote " Strike down all limits on our perceptions that chain us to the mundane world! "
but it also was able to deliver us (what I consider) the best way to enjoy the story consearing on how the events where shown to us (timewise).
Hence.. why I definitly say.., the best order to watch Haruhi and enjoy it to its full potential is definitly.. "as aired on T.V.".
Also.. in the end.., with Kyon's little remark on each episode.., we never ended up beeing lost
And True fact is.., if the episodes (giving the same content), where to have been displayed properly.., I recon many would have lost a bit of the excitement of wanting to see the next episode just so it could show us what happened prior to the others we had seen; myself included
Edit :
Needed to fix the order due to all the confusion..
Now I just hope I got it right ^^