Got similar problem with german characters on my mac. In OS X I use KeyRemap4Macbook. It allows to set remapping based on the the current application - so I use the default mapping for most apps - but set to specific mappings for my programming. Also you can map left and right modifier keys separately (getting one Alt and one Alt-Gr eg)
I have been looking for a similar app for Windows - but couldn't find so far. I remember seeing a similar tool for linux - but can't recall the name.
update maybe check the options presented at alternativeto - there seem to be some for any os.