From what I've heard, Agilent probably has the best software and the most durable and user-friendly instruments. Waters and Shimadzu are cheap so I guess they got that going for them, but I've seen more broken Waters and Shimadzu machines than working ones. Sciex/Danaher has very sensitive instruments, but crap software and they tend to come in on the expensive side. Thermo has the edge in terms of hardware, but they are much more expensive than the rest of their competitors, and I haven't heard great things as far as software goes. There's also Bruker now, and they have some unique instrument capabilities, but they are based in Germany and don't have the best support stateside.