For me, the transition to lion was relatively painless. Painless here basically means that I patched up the couple of things that gave me problems . In the specific situation, the issue is that Apple's new developer's tools do not include regular gcc anymore. Instead there is a version working with llvm backend which is great but has some issues with some packages that have not been updated yet.
Another problem is that is closely related is that I had a Python 2.7 installed with Python main website package. I did this because older OS Xs did not have Python 2.7. That Python was built with the older gcc-4.0 apple shipped with SL. Thus, new libraries I install with pip still want that compiler, which apple moved in /Developers-3.2.x/... Thus, I lived so far adding that directory to the PATH and happily compiling.
What I should have done was getting rid of my beloved python and either use EPD or Apple built-in 2.7 (shipping with Lion) or use a brew-ed python or see if Python.org distributes a Python compiled with the new compiler (which, as far as I know, is perfectly capable of building Python). The question is: are there any python extension I need that need the older gcc? But this is not something I'm going to discuss here: not yet ready to make the transition.
I just want to point out that I installed the old gcc from homebrew-alt, and now I can just brew install --use-gcc for packages that need the old gcc compiler. This is easy to use and nice. I also removed the old Developers and hope everything's fine.
% git clone https://github.com/adamv/homebrew-alt.git /usr/local/LibraryAlt % brew install /usr/local/LibraryAlt/duplicates/apple-gcc42.rb
An older version of gfortran I installed conflicted, but the commands above worked like a charm after removing it.