icnurse07,
Last year in May of 2007 I sent in my I-129 Extension of TN Status. It eventually got approved on July 31, 2007. I had travelled back to Canada in mid-June 2007 to attend a friends wedding (1 month after submitting the I-129, and 1 month before it's eventual approval).
Upon my return to the US (with roughly 30 days left in my current TN at the time) I entered on my existing TN with no hassles at all. No mention of the I-129 petition was even made at the border upon my return and I was waved through no problem. As previously stated, my mail-in TN (I-129) was eventualy approved in July 2007 so travel to Canada with a pending I-129 for TN status was not an issue for me then and should not be an issue for you.
As Warlord mentioned, it would be good to carry a fresh TN application package with you just in case. When I went back to Canada for the weekend last June I had brought my documents to apply for a TN at the border JUST IN CASE the border guard, as nelsona mentioned, would offer to process a fresh TN at the border. However this was not the case for me but it was good to be prepared just in case (it doesn't really take to long to prepare a proper TN application package anyways).
Hope this helps,
CJ