Xeon E5450 should have exactly the same die as QX9650. However, some differences do exist between them.
One of the major difference between them is multiplier. Xeon should feature a locked multiplier, while QX9650's is unlocked. This allow enthusiasts to overclock QX9650 more easily.
On the other side, due to Xeon's higher binning, E5450 should be a lot more stable than QX9650, while possibly churning out less heat. Xeon also features a different socket than QX9650 (LGA 771 for Xeon, LGA 775 for QX9650). Xeon systems also use different RAM than QX9650 (FB-DIMM vs. DDR2/3).
Other than that, both should perform relatively the same at stock setting.
Personal suggestion: If you're looking for performance, and not that much on stability, then I would recommend QX9650. The entire system cost should be lower than Xeons, due to cheaper motherboard and cheaper RAMs (DDR2/3 vs. FB-DIMM). You can get a decent aftermarket air cooler, and overclock QX9650 to 4.0Ghz. Although it probably won't be as stable as those Xeons used in data-centers and servers, but if you can tolerate one crash or two in a year, than QX9650 would be a better choice.
EDIT:
Due to the nature of both processors, there's no direct comparison between them. However, there are benchmarks for them against other processor in their genre.
QX9650 w/ desktop applications (audio / video editing, games, etc)
http://techreport.com/articles.x/13470
E5450 w/ server applications (SPECjbb, etc)
http://techreport.com/articles.x/13224