Hmm...
This is an interesting quesiton, and finally one I feel comfortable responding to, after tons of reading and asking questions.
I totally agree with the jacket/case thing being a quesiton of what message you're trying to get across, but I disagree that one or the other is going to seem more "professional." A lot of indie lables and "indie" lables (i.e. sub-lables under Sony, BMG, etc.) purposefully put their albums in jackets or paper cases similar to jewel cases, because the purchaser is looking for something that looks and sounds less produced, and therefore not "tainted by money" or however they look at it. Some people, however, will think that a CD in a jewel case has had more money put into it, therefore showing that it's not some shitty demo recorded by your 12-year old brother in your grandma's basement with a single mic. It depends on who you want to buy your product.
Personally, I believe that it's not the type of packaging, but whether or not the product itself looks professional, that counts. I buy CDs in both forms of packaging, but I keep all my CDs in binders anyway, and prefer the ease of storing jackets over jewel cases. I have a huge stack of jewel cases that I don't know what to do with.
That's my two cents.