Short answer: Go 64-bit if you can, which is faster than both PAE/non-PAE 32-bit; if you cannot, non-PAE may be 1-2% faster than PAE.

In theory PAE has a slight overhead over non-PAE...

• The big advantage of PAE is allowing a 32-bit processor/system to use more than 4GB of RAM


• But this requires slightly more overhead over non-PAE, which can lead to slightly decreased performance.
  
  
  
  • Here's a very simple explanation: in non-PAE mode, a 32-bit CPU must lookup (access) two tables to access a physical memory address; in PAE-mode, it must lookup three tables to do so. The one additional lookup requires some (very small) extra time, thus imposing additional overhead.
  
  
  • At the end of this answer are two images from the Wikipedia PAE article, illustrating the above point.
  
  
  • NX/XD bit: The PAE kernel also supports the No-eXecute/eXecute-Disable bit on 64-bit processors; this can help prevent some kinds of virus/malicious attacks (buffer overflows), but IMO this doesn't matter much when choosing 32-bit kernels for Ubuntu.
  
  
  
  

...but in practice this overhead is negligible (almost nothing)...

• Phoronix has done a number of tests over the years which show that on systems with 4GB or less, the PAE kernel may be at most approximately 5% slower than the non-PAE kernel. This is only for a specific test application; the usual difference is less than 1%.
  
  
  
  • Tests for 12.04 LTS - 8 GB system!
  
  
  • Tests for 11.04 - 4 and 8GB systems
  
  
  
  

and 64-bit almost always beats BOTH 32-bit kernels - go for it!

• The one thing those Phoronix benchmarks above tell you is that 64-bit is king -- even if you have less than 4GB of RAM (although I'd recommend 1GB as the minimum)


• If you have a 64-bit processor -- generally anything after 2006 except Intel Atoms -- you are probably losing performance by using a 32-bit kernel!

Comparing non-PAE vs. PAE page table accesses:

1. Non-PAE

   
   

   

   
   



2. PAE