(Comment by me in response to post at FSP)
I've seen several seminars about negotiating start-up packages, and they have all advised candidates to do the money negotiations once the offer is made.
I've also talked to several post docs on the job market, and know that interviewers usually want some start-up estimate from the candidate before making an offer, which makes sense. If the university can't offer the kind of money necessary to do the research, the university and the candidate are not a good match.
The seminars I've seen also advise the candidate to *definitely* negotiate salary. I always thought it would be much easier (and much more admired) to negotiate for all the start-up package stuff, other than the salary. All the other stuff is all about getting great science done. The salary seems just selfish. But, it was explained to me this way: 1) the university *expects* you to negotiate the salary, so the offer is lower than they are prepared to offer, and they're surprised when you don't negotiate, and 2) negotiating to a salary that is fair and comparable makes the candidate/employee feel valued, loyal to the organization, and allows the candidate/employee to not waste time/energy worrying about salary.