You need to look closely at your application, and decide what features are most important, whether it be power usage, low-cost, etc. Then look at the available FPGA's in your price bracket and see which ones suit your needs most closely.
If you were from Synopsys camp, then Altera may look appealing due to the constraints in Altera is the same as Design Compiler. However in Xilinx you need to twist your mind when constraining setup/hold time delay.
I do prefer Xilinx 'coz of its resources. But I think Altera iz gud and morever they had opened an R&D in my country, Vietnam Now I'm doing both on Altera's and Xilinx'
Both Altera & Xilinx have comparable technology & parts in terms of FPGA & CPLDs. The issue is usually the IP & the tools: Xilinx ISE vs Altera Quartus.
EU folk seem to favor Xilinx while US prefer Altera - can't explain it so just sharing an observation. Neither is better nor worse. I think most engineers will favor the IDE and from there the actual product. I like Quartus better than ISE but that's just me, plus my geographic opinion could have something to do with that seleciton too