What would be appropriate to give to my nephew, who has obtained a Doctorate in chemical and biological engineering?

A card and this shirt http://www.thinkgeek.com/tshirts/sciencemath/2891/ might

It’s a shirt on Think Geek showing the caffeine molecule (very nerdy and appropriate for a biological engineer who just might be a “user”.

While we’re on the topic of shirts, This is one of my favorites, and might just work depending on your nephew’s sense of humor.

Nice one Hobbes!

Something that will not make him feel as a library nerd… like a parfum, or a very nice tie+shirt

Honestly, I really believe that cash is King. With a nice letter or note, it would be appreciated. Even a small gift, like a book on how to write professional letters/memos for techies or something—- with CASH.

An engraved iPod?

anything that will help release stress – something like a vibrating/massaging chair back, he will probably need these things as he is going to be flying high