AVRDude open source command line programming tool is well known among AVR developers. It supports long list of official and non official AVR programmers. The only disadvantage in it that it lacks graphical user interface. Of course there are lots attempts to make GUI for avrdude but still non of them seems to be completed or very user friendly. Some of them are programmer adapter oriented like eXtreme Burner that runs with usbasp programmer.
If you can’t find GUI that suits you, check out another interesting web based interface. It is still in deep alpha but already gives intuition on looks ant usability. Currently with AVRweb you can only read and change avr fuse settings. But there are more features planned as makefile support to build and program targets, intelligent URL support for flashing chips by clicking on links. Might be more ideas will come up. Of course setting it requires standard web server package to be installed such as Apache, PHP5 and SQlite. But once set you can open UI and program AVRs directly from your iPad or other android device.