There are only a few certs that I know about CHFI, GCFA, and EnCE. From your experience or knowledge, can you tell me which one you would prefer and why?

Thanks

Think about it in regards to what the certs actually mean.  The GCFA and others like it are meant to show that you're very familiar with the process of forensics and generally familiar with a variety of tools.  The EnCE and others like it are meant to show that you're very familiar with one tool and generally familiar with the overall process of forensics. 

If you're focusing on traditional forensics and face a lot of time on the witness stand, a tool based cert (eg. EnCE) will go far since the opposing lawyers will spend a lot of effort trying to find weaknesses in the various tools and processes you use as well as your experience with each.  If you have a cert in a well known, vetted product like EnCase and you follow your checklists to the letter it is hard to get yourself in trouble and hard for them to portray you as being unskilled/unfamiliar with your tools.

If you're focusing on non-traditional forensics (more incident response focused and less litigation focused) then the general certs will probably go farther as they suggest that your skillset is broad versus deep. (familiar with a lot of tools and platforms rather than being an expert witness in one specific tool)  You can also specialize with additional certs like the GREM for malware, network forensics, etc.  Please note that I'm implying that much of this is about appearances.  I know folks that are skilled in both areas, but many people will eventually choose to favor one path over the other.

This book was refered to me by a Sr Computer Forensics Analyst years ago and then a few months later in school this was the one we used as the book for the class.  Very good book

http://www.amazon.com/Digital-Evidence-Computer-Crime-Third/dp/0123742684/ref=sr_1_6?ie=UTF8&qid=1323818518&sr=8-6

Think about picking it up.