Apple Mail freezes the entire system

This just started today after absolutely no problems with my system in the last 20 months of ownership.
This morning I got the spinning beach ball and my computer became completely unresponsive. I could not force quit any apps or switch between them. I thought it was something to do with iTunes because it tends to be less than snappy at start up due to a lot of music and video however, that wasn't the issue. After a few hours of messing about, disconnecting peripherals and turning off time machine it became evident that Apple Mail was causing the trouble.
I'm pretty good at pruning my mail and emptying the trash and I've also used disk tools to repair the disk permissions. I don't save drafts to the server and I don't add invitations to iCal.
I haven't added any new applications and the only recent update was the iTunes update that I installed after the trouble started.
As long as I don't launch Mail, the computer is golden. If I do launch it there is a minimum of 5 minutes of innactivity and at any time it might go awry and cause another 3 - 5 minute period of completely useless innactivity.
Any thoughts? I know Mozilla will take over quite nicely but I don't want to switch mail clients because Apple Mail has been just fine since I started using it with exception to today.
Thanks,
Andrew

Hi, I haven't actually tried this in 10.6.x, or maybe I have & forgot!
Not certain, but this can fix myriad Mail problems...
Safe Boot from the HD, (holding Shift key down at bootup),  it will try to repair your Disk Directory while the spinning radian is happening, so let it go, run Disk Utility in Applications>Utilities, then highlight your drive, click on Repair Permissions, then move this folder & file to the Desktop.
Move this Folder to the Desktop...
/Users/YourUserName/Library/Caches/Mail/
Move this file to the Desktop...
/Users/YourUserName/Library/Mail/Envelope Index
Reboot.
If that doesn't do it and you can afford to redo all your Rules, try these & reboot...
/Users/YourUserName/Library/Mail/MessageRules.plist
/Users/YourUserName/Library/Mail/MessageRules.plist.backup

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        GL_EXT_texture_lod_bias, GL_EXT_texture_object, GL_EXT_vertex_array,
        GL_APPLE_packed_pixels, GL_IBM_rasterpos_clip,
        GL_IBM_texture_mirrored_repeat, GL_MESA_window_pos, GL_NV_blend_square,
        GL_NV_light_max_exponent, GL_NV_texgen_reflection, GL_OES_read_format,
        GL_SGI_color_matrix, GL_SGI_color_table, GL_SGIS_texture_edge_clamp,
        GL_SGIS_texture_lod
       visual  x  bf lv rg d st colorbuffer ax dp st accumbuffer  ms  cav
    id dep cl sp sz l  ci b ro  r  g  b  a bf th cl  r  g  b  a ns b eat
    0x22 24 tc  0 32  0 r  y  .  8  8  8  8  0 24  8  0  0  0  0  0 0 None
    0x23 24 tc  0 32  0 r  .  .  8  8  8  8  0 24  8  0  0  0  0  0 0 None
    0x24 24 tc  0 32  0 r  y  .  8  8  8  8  0 16  0  0  0  0  0  0 0 None
    0x25 24 tc  0 32  0 r  .  .  8  8  8  8  0 16  0  0  0  0  0  0 0 None
    0x26 24 tc  0 32  0 r  y  .  8  8  8  8  0  0  0  0  0  0  0  0 0 None
    0x27 24 tc  0 32  0 r  .  .  8  8  8  8  0  0  0  0  0  0  0  0 0 None
    0x28 24 tc  0 32  0 r  y  .  8  8  8  8  0 24  8 16 16 16 16  0 0 Slow
    0x29 24 tc  0 32  0 r  .  .  8  8  8  8  0 24  8 16 16 16 16  0 0 Slow
    0x2a 24 tc  0 32  0 r  y  .  8  8  8  8  0 16  0 16 16 16 16  0 0 Slow
    0x2b 24 tc  0 32  0 r  .  .  8  8  8  8  0 16  0 16 16 16 16  0 0 Slow
    0x2c 24 tc  0 32  0 r  y  .  8  8  8  8  0  0  0 16 16 16 16  0 0 Slow
    0x2d 24 tc  0 32  0 r  .  .  8  8  8  8  0  0  0 16 16 16 16  0 0 Slow

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