Hi, there was a discussion on this top in the Linkedin Hydrogeology Forum, I have included a few of the comments given that are relevant to aquifer modeling and GIS. Modflow is the popular and best documented. GRASS would be my second port of call.
The USGS ModelMuse software is a great, free GUI for managing MODFLOW input and output data. It can interface with GIS data and has many features comparable to commercial MODFLOW GUIs.
http://water.usgs.gov/nrp/gwsoftware/ModelMuse/ModelMuse.html
I would recommend you look at Interactive Ground Water. You can download it at http://www.egr.msu.edu/igw/
You can 'find many free ware programs at the following address:
http://water.usgs.gov/ogw/gwrp/activities/gwmodel_dev.html
I find it very useful Modflow
A free version of Processing Modflow (PMWIN 5.3.2) is available in http://www.simcore.com/pm53 It supports MODFLOW-88/96, MT3DMS, PEST, etc. The version is a little dated. Nevertheless, it runs on Windows 7 and XP.
If anybody is still interested, i saw that the latest version of GRASS ( GRASS 6.4.2RC3) software has a tool for groundwater analysis. You can download it from here
http://grass.fbk.eu/.