When you remove packages make sure you uninstall them from the command line using "apt-get purge <packagename>" this will remove the configuration files along with the package. After that it depends somewhat on how well behaved the packages were, packages can run scripts on installation and removal which can make arbitrary changes to the system if necessary, and if badly written they may not clean themselves up properly when you remove the package. You can also use "apt-get install <packagename> --reinstall" to reinstall any packages whose files you think may have got messed up or corrupted.

It is possible to get back to a clean state without reflashing, but depending on the state of your current install it can take quite a bit of in-depth knowledge. Quite honestly flashing is easier.

If your having problems with flashing because of Windows 7, then grab yourself a spare 1GB+ USB stick, a copy of unetbootin and use unetbootin to install a version of ubuntu to your USB stick. Also check out the flashing guide and download the flasher deb and the rootfs image (and optionally the eMMC image) and save them to your USB drive just in case you can't get networking when you boot the USB stick. I've just noticed this is quite similar to option 4 of what you can do if you have the 64-bit version of Windows 7. There are other options for flashing in this situation in the wiki which you could also use.