I have just started learning how to Program AVR's myself and I went for Atmel Studio 4 as I understand it Atmel Studio 6 is just an improvement in the IDE you might be better starting with AS4 over AS6 as there are plenty of tutorials covering AS4 ... and according to all the googling I have done AS5 has some problems so AS4 or AS6 .. as for eclipse and AVR dude I tried AVR Dude it was not for me and Eclipse I find that horrendous to use (all down to personal preference in the end) as for GCC, Atmel Studio's toolchain uses GCC and so does AVR dude and I'm sure Eclipse also uses GCC (well depending on plugin I assume) so that's not really an issue.
what you really should Be deciding is C/C++ or ASM for AVR(8/16bit) Programming.
just my 2p's worth
zx