I think I may know what is causing the problem, because it happened to me when upgrading from OSX 10.6 to OSX 10.8.
You probably have Sublime CodeIntel plugin installed. Try removing it. This should make things fast again.
If you still want to use CodeIntel, the problem may be that you have some kind of huge binary file that it is trying to index (possibly for the first time). Check out this issue on CodeIntel's github page: https://github.com/Kronuz/SublimeCodeIntel/issues/215
. Another option is to try to let it index for a while; maybe it will speed up after that.