I have a number of linux based embedded microcontroller examples at github https://github.com/dwelch67. Note the ide is your favorite text editor and a command line where you type make.
Note the free tools for microchip (pic32) (not the ones FROM microchip) have optimization, 16 bit instruction set support, etc. And you get to see what is going on (cause you are doing it yourself). These of course being the mainline gcc and llvm (not the ones from microchip).
The mbed or stellaris are probably more along the lines of what you want. Or arduino like go with the maple perhaps. I hate to say maybe the fez panda. The msp430 launchpad is $4.30, at that price might as well buy a couple to save for a rainy day. The stm32 value line discovery is around $10, same deal get one save it for a rainy day.
If you let the libraries and environment do all the work for you then its no different than just writing applications on your desktop computer, a bit of a waste of time going embedded, just write desktop apps. If you go with embedded you should roll up your sleeves and get your hands dirty...something to think about...Otherwise just buy the arduino and get it over with. Atmel is hard to touch for customer satisfaction, not sure why but it is what it is. The avr instruction set is not great, nowhere near as bad as the PIC (not counting the PIC32) but not as good as the msp430 or ARM instruction sets. I have used the arduino ide on linux, likely wont need to reboot to windows. There isnt anything as easy as the arduino except maybe the BASIC based stamps like parallax and some others.
As with linux/unix development in general, dont focus on looking for an IDE. Focus on the compiler, gcc or llvm, then your favorite editor and thats it, start coding. Apply that to a microcontroller and look at the targets the compilers support. ARM and MIPS are a natural fit, you wont have any problems getting the tools up and running, any time you are taking a patched gcc versions and trying to make that work on your up to date Linux box you are going to struggle from time to time, avr, msp, and pic fall into that category. Same goes for sdcc, it is hit or miss, and anyway you have to ask yourself: C on the 8051? Not as bad as C on the PIC but close. If you are really looking for a polished, supported, up to date, stable IDE, etc, you have to go to windows. Keil, IAR, Code Red, etc. The demand just isnt there, linux/unix developers historically spend their time arguing vi vs emacs as those are the dominant ides for lack of a better term. throw in gdb if you get desperate.