Early 996's suffer from 3 things.
1) Supply. Lots of these cars were made and that supply drives down prices. Also most cars are now old enough that they are being sold by either original owners or early second owners. Many of these are not enthusaist owners, but people who need the latest/coolest so just want to sell and buy the next latest and greatest.
2) Maintenance fears. Alot was made of the maintenance issues on these early 996's. I think of it is overblown as these cars have issue like all Porsche do. The 993 and 964 varianats are not without their own issues too. Many forget that.
3) Appeareance cool factor. Many Porsche folk dislike the addition of water cooling and from day 1 with 996 did not like its look or interior. Many felt it was mass produced junk compare to their "hand crafted" 993. As such it never garnered the love of the enthusaist communuty. It is that community which provides the stable long term value. If it does not exist the car will deprciate like any 10 year old car. The 944, 944 Turbo and early 928 all suffer this same fate. However these front engine watercooled cars have develop and entirely new following precisely because their value has dropped. The 944 Turbo for the last 10 years has been around 10k to buy and at 10k makes an amazing performance bargan even today.
So feel the 996 is underrated in the Porsche community the same way the early boxsters are. It is a great time to buy one, but still be ware they are expesnive cars and can require expensive maintenance. This should not scare you, but you MUST factor it in or else you experience will not be a good one.
Now I can't say it is the best time to get a 996 and I still see prices dropping, but you car get alot of car for this money.