'git bisect' says this commit caused the segmentation faults:
a37b2219d6e3f299379c6434d65f300660d12c3e is the first bad commit
commit a37b2219d6e3f299379c6434d65f300660d12c3e
Author: Brian Paul <brianp@vmware.com>
Date:   Thu Jun 10 20:23:03 2010 -0600

    mesa: refactor shader api / object code
    
    Remove the unneeded ctx->Driver hooks for shader-related functions.
    Move state and API-related things into main/.

:040000 040000 140d9276ce7da08708770dbd2403da2902a79794 75d7f0a946d0ed054c247fd3d768a3a233cf5afa M      src

Here is my bisection log:
git bisect start
# good: [5b1330eaf4af0f51cc3326801b2fd260f24cf136] Merge branch 'master' of git://anongit.freedesktop.org/mesa/mesa
git bisect good 5b1330eaf4af0f51cc3326801b2fd260f24cf136
# bad: [5d1cc930779936a475495284a496f5457f67a939] r300g: a couple more chipsets do not have HiZ RAM
git bisect bad 5d1cc930779936a475495284a496f5457f67a939
# good: [6acd2117c1b5700077b2220623a06d89fa5c14a7] r300g: more informative warning in END_CS
git bisect good 6acd2117c1b5700077b2220623a06d89fa5c14a7
# good: [256097858881323d0b6ece248be163bb157f43aa] configure: Add galahad to default build.
git bisect good 256097858881323d0b6ece248be163bb157f43aa
# good: [7315300fa5a5e63c16b9e258feb4df76176b5b4b] gallium/docs: document TGSI_SEMANTIC_EDGEFLAG
git bisect good 7315300fa5a5e63c16b9e258feb4df76176b5b4b
# skip: [ec2b92f98c2e7f161521b447cc1d9a36bce3707c] mesa: rename src/mesa/shader/ to src/mesa/program/
git bisect skip ec2b92f98c2e7f161521b447cc1d9a36bce3707c
# bad: [ca12aefdacd22fb42e3f1d3852db4c12de886554] Merge branch 'shader-file-reorg'
git bisect bad ca12aefdacd22fb42e3f1d3852db4c12de886554
# skip: [f1c5043f94261fecd8a6e54fe37d786554affcdd] mesa: move shader/slang/* sources to main/slang/*
git bisect skip f1c5043f94261fecd8a6e54fe37d786554affcdd
# skip: [7936e06657bc43de80ae4f56ee9db956e193d880] mesa: move nvprogram.[ch] to main/
git bisect skip 7936e06657bc43de80ae4f56ee9db956e193d880
# good: [93bce03b275f66b6b2db410bbef38954de6a617c] r300g: separate the cache flush from the framebuffer state
git bisect good 93bce03b275f66b6b2db410bbef38954de6a617c
# skip: [412cddf954d35282f913d01d83d3cdb45cf0e2d0] mesa: move arbprogram.[ch] to main/
git bisect skip 412cddf954d35282f913d01d83d3cdb45cf0e2d0
# good: [f2122d47248e59a0f23c15d7f647d7e2072c8d79] r300g: remove an XXX comment
git bisect good f2122d47248e59a0f23c15d7f647d7e2072c8d79
# bad: [936605fc8a69f67de323e5ede60c2f1373bfcafe] mesa: move uniforms.c to main/
git bisect bad 936605fc8a69f67de323e5ede60c2f1373bfcafe
# good: [050eed095a3f7eaeada1e292f92f2b549d74963f] i965: remove UseProgram driver callback
git bisect good 050eed095a3f7eaeada1e292f92f2b549d74963f
# bad: [a37b2219d6e3f299379c6434d65f300660d12c3e] mesa: refactor shader api / object code
git bisect bad a37b2219d6e3f299379c6434d65f300660d12c3e

Try running 'make clean' and then rebuild mesa.

autogen and make clean fixed it, thanks. (origin/master works too now)