Yes.
But this varies all over the place both in how much general flexibility there is and in terms of which items are negotiable. Some places have union scales and very little is negotiable. At other places, everything is open. What can be bargained over depends not only on the department, but also on institutional rules. What's more, sometimes resources come at the expense of the department and sometimes they come at the expense of the institution higher up.
Sometimes you need a credible outside option to get a concession. Sometimes you just need an outside option, even if you're not very likely to take it, because the department would like an excuse to give you something. And sometimes all you need to do is ask. (Have a real need for a bigger computer to get your work done? They might give it to you because they want you to be successful!)
Do remember that this kind of negotiation is part of a repeated game. If the department is very difficult about it, that tells you something. (If you're difficult, it tells the department something.)
