This problem has been happening since at least 13w39a for me. Upon launching the game from the launcher the Mojang splash screen will appear and will not go away for a very long time, sometimes as much as 20+ minutes. Eventually it will start the game and things will run normally.

Then, when I stop the game, it will hang up a second time, again for nearly as long as the first time. During both times the window will become unresponsive and the only way to stop the program is to kill it with the task manager.

Returning to the regular non-snapshot version corrects this issue, and the game will start in only a couple of seconds.

EDIT: The log from the terminal when launching the game shows this when it hangs:

Looking for old natives to clean up...
Deleting /home/arfink/.minecraft/versions/13w41a/13w41a-natives-217644539061466
Unpacking natives to /home/arfink/.minecraft/versions/13w41a/13w41a-natives-218838299203305
Launching in /home/arfink/.minecraftsnaps2
Running /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java -Xmx1G -Djava.library.path=/home/arfink/.minecraft/versions/13w41a/13w41a-natives-218838299203305 -cp /home/arfink/.minecraft/libraries/java3d/vecmath/1.3.1/vecmath-1.3.1.jar:/home/arfink/.minecraft/libraries/net/sf/trove4j/trove4j/3.0.3/trove4j-3.0.3.jar:/home/arfink/.minecraft/libraries/com/ibm/icu/icu4j-core-mojang/51.2/icu4j-core-mojang-51.2.jar:/home/arfink/.minecraft/libraries/net/sf/jopt-simple/jopt-simple/4.5/jopt-simple-4.5.jar:/home/arfink/.minecraft/libraries/com/paulscode/codecjorbis/20101023/codecjorbis-20101023.jar:/home/arfink/.minecraft/libraries/com/paulscode/codecwav/20101023/codecwav-20101023.jar:/home/arfink/.minecraft/libraries/com/paulscode/libraryjavasound/20101123/libraryjavasound-20101123.jar:/home/arfink/.minecraft/libraries/com/paulscode/librarylwjglopenal/20100824/librarylwjglopenal-20100824.jar:/home/arfink/.minecraft/libraries/com/paulscode/soundsystem/20120107/soundsystem-20120107.jar:/home/arfink/.minecraft/libraries/io/netty/netty-all/4.0.9.Final/netty-all-4.0.9.Final.jar:/home/arfink/.minecraft/libraries/com/google/guava/guava/14.0/guava-14.0.jar:/home/arfink/.minecraft/libraries/org/apache/commons/commons-lang3/3.1/commons-lang3-3.1.jar:/home/arfink/.minecraft/libraries/commons-io/commons-io/2.4/commons-io-2.4.jar:/home/arfink/.minecraft/libraries/net/java/jinput/jinput/2.0.5/jinput-2.0.5.jar:/home/arfink/.minecraft/libraries/net/java/jutils/jutils/1.0.0/jutils-1.0.0.jar:/home/arfink/.minecraft/libraries/com/google/code/gson/gson/2.2.2/gson-2.2.2.jar:/home/arfink/.minecraft/libraries/com/mojang/authlib/1.1/authlib-1.1.jar:/home/arfink/.minecraft/libraries/org/apache/logging/log4j/log4j-api/2.0-beta9/log4j-api-2.0-beta9.jar:/home/arfink/.minecraft/libraries/org/apache/logging/log4j/log4j-core/2.0-beta9/log4j-core-2.0-beta9.jar:/home/arfink/.minecraft/libraries/org/lwjgl/lwjgl/lwjgl/2.9.0/lwjgl-2.9.0.jar:/home/arfink/.minecraft/libraries/org/lwjgl/lwjgl/lwjgl_util/2.9.0/lwjgl_util-2.9.0.jar:/home/arfink/.minecraft/versions/13w41a/13w41a.jar net.minecraft.client.main.Main --username arfink --session token:008b373c78ee4a2c83c54a8a46bfddc0:ef2b6b43bad840b3872e44f282d7efea --version 13w41a --gameDir /home/arfink/.minecraftsnaps2 --assetsDir /home/arfink/.minecraft/assets --uuid ef2b6b43bad840b3872e44f282d7efea --accessToken 008b373c78ee4a2c83c54a8a46bfddc0
Client> [22:48:07] [main/INFO]: Setting user: arfink
Client> [22:48:07] [main/INFO]: (Session ID is token:008b373c78ee4a2c83c54a8a46bfddc0:ef2b6b43bad840b3872e44f282d7efea)
Client> Completely ignored arguments: [--session, token:008b373c78ee4a2c83c54a8a46bfddc0:ef2b6b43bad840b3872e44f282d7efea]
Client> [22:48:08] [Client thread/INFO]: LWJGL Version: 2.9.0
Client> [22:48:08] [Client thread/INFO]: Reloading ResourceManager: Default
Client>
Client> Starting up SoundSystem...
Client> Initializing LWJGL OpenAL
Client> (The LWJGL binding of OpenAL. For more information, see http://www.lwjgl.org)
Client> OpenAL initialized.
Client>