First off, I suggest you check the tech articles section of this website. It contains many great articles on engine swaps, drivetrain swaps, and general resto-modding of the E9. Firstfives.org also has an excellent 2.8->3.5 swap article, with pictures and how to upgrade the fuel injection system.
Next, this is perhaps one of the top three most common questions about E9s. There have been several threads on this topic in the past, ranging from what transmission to use to what engine to use. Search through the old posts, you will find many opinions on the matter, probably much faster than by asking it again.
Lastly, the answer to your question varies largely with how much money you want to spend. The best swap is in the 10K range, at least. The "worst" swap can be done for less than 400$. Also, you have to decide if you want to keep your E9 original, or build it to your tastes. I did my swaps because the originality was already shot when I got it. (bought with a blown engine)
