Id say the most important thing to look out for is the automatic transmission, they generally fail. Ive had three e46s and all of them have had transmission problems. Drive the car before buying it, check the transmission shifts smoothly, check that reverse engages, lift the car so you can see that it hasnt been hit underneath.
Other than that the electric windows sometimes fail, check the suspension also, most e46 wont last more than 50,000 miles with good suspension.
As for packages id say look into the facelifted version (02 +) the 99-01 seems to start to look old in my opinion.