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In comments on this question, Mr. Wizard suggested a community wiki to share the bug fixes/workarounds (or possibly other tricks) people load in their init.m. I think this could provide a nice resource.

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I think this should probably be restricted to bug fixes and workarounds or it becomes too broad. –  Mr.Wizard Aug 16 '13 at 21:54
    
Should these be version-tagged? –  Yves Klett Aug 17 '13 at 16:54
    
@Yves I think they should, and so far it looks like everyone has already done that. –  Mr.Wizard Aug 17 '13 at 20:51
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3 Answers

As a version 7 user these likely don't apply to most users but here are mine:

  • Fix Symbol name slow-down weirdness (hashing problem?):

    SetSystemOptions["NeedNotReevaluateOptions"->{"UseSymbolLists"->True}];
    
  • Fix a bug in FullSimplify:

    Unprotect[Holonomic`HolonomicFullSimplify];Clear[Holonomic`HolonomicFullSimplify]; 
    
  • Prevent Mathematica from eating all my RAM and freezing (most of the time):

    $Pre = Function[Null, MemoryConstrained[Unevaluated @ #, 2^32, "Memory Exceeded"], HoldAll]
    

I believe I used to have a few more but I must have removed them because either they caused problems or because I found them unnecessary.

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Here is one that came from a Wolfram employee so it should be safe to add in version 9:

FindInstance returns Indeterminate in version 9, but not in 8

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Here's a patch from Adam Strzebonski of Wolfram, which fixes a bug in RootReduce in 9.0.1.

ToNumberField won't recognize Root as explicit algebraic number

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