I upgraded the operation system of a Mac mini at work from 10.9 Mavericks to 10.10 Yosemite this morning. I already did it once to my Macbook Pro and the upgrade was smooth, but it went so well because I just don't use my MBPR as much as my Mac mini. Here's some troubleshooting guide for you.

Pow

Effect Don't work
Cause ipfw has been removed in favour of pf in Yosemite, thus Pow is not able to leverage it.
Fix Uninstall and Re-install Pow will fix it since the latest release 0.5.0 fixes the issue. https://github.com/basecamp/pow/issues/452

Homebrew

Effect brew produces errors and doesn't work.
Cause Yosemite ships Ruby 2.0 instead of 1.8 and brew command expects ruby interpreter to be at a specific path.
Fix The latest version of Homebrew doesn't have this issue. Hit brew upgrade before you perform an upgrade, otherwise you will have to re-install it. https://github.com/Homebrew/homebrew/issues/29795

RubyMine

Effect Unable to launch RubyMine.
Causes Java runtime does not exist on a newly installed OS X 10.10.
Fix Download and install Java Runtime from http://support.apple.com/kb/DL1572.

iTerm2, Zsh, Git

Effect git commands don't work on iTerm2 with zsh.

/usr/local/Cellar/git/2.1.2/libexec/git-core/git-pull: line 11: git-sh-setup: No such file or directory

Cause iTerm2 does some interesting things when initiation a shell(zsh). http://stackoverflow.com/questions/24022582/osx-10-10-yosemite-beta-on-git-pull-git-sh-setup-no-such-file-or-directory
Fix Upgrade iTerm2.

Rbenv & ruby-build

Effect rbenv install or ruby-build produces errors like below:

Last 10 log lines:
checking for clang... clang
checking for gcc... (cached) clang
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... configure: error: in `/var/folders/wj/x_5r7xts0_qgj_75mghwq63h0000gs/T/ruby-build.20141023175933.45125/ruby-2.1.0':
configure: error: cannot run C compiled programs.

또는

Last 10 log lines:
1 error generated.
make: *** [miniinit.o] Error 1
1 error generated.
make: *** [miniprelude.o] Error 1
1 error generated.
make: *** [class.o] Error 1
1 error generated.
make: *** [complex.o] Error 1
1 error generated.
make: *** [bignum.o] Error 1

Cause gcc compiler issue. https://github.com/sstephenson/ruby-build/issues/651
Fix 1. xcode-select --install.  2. CC=/usr/bin/gcc rbenv install 2.1.1