I also work at a university, and we are in the process of removing everybody's admin rights. I went to senior staff (who then went along with my plan) with the following arguments:
1) Security; Viruses have a much harder time infecting computers if the user is running without local admin rights.
2) Liability; Does your college have licenses for Mathematic, ArcGIS, SPSS, etc? or are your professors using their own license? if it's their own, are they using it correctly? (i.e. only installed on one computer per license) and more importantly, can you prove it if you were audited.
3) "CrapWare"; we had people installing stuff (think free games) that was eating up massive support time, because it came with ad-ware/spy-ware/what-have-you-not-ware and we were expected to support it.
4) forcing loadouts. We use sophos (and have been happy with it), but we had a small number of people that had uninstalled our enterprise version of Sophos, and had installed their own internet security suite. This cause all sorts of problems when it's firewall started blocking certain AD traffic, and other tools that we have on all machines.
That being said there are some software packages that *need* admin rights. MS Great Plains is one, so our financial people have to have admin rights on their computers. I've also discovered that the Kodak Easy Share software really wants admin rights, right now I'm trying to find a way around that.
the flip side is that we had to effectively guarantee 24-hour turn around on all software install requests (within reason) so far I've been happy with the results.
As for the specialized software, try to get campus licenses (perhaps concurrent licensing for some of the more esoteric packages) and either install it everywhere, or (depending on your setup) have it fall under advertised software, so that if they need it, it can be installed automatically for them without the need for admin rights.