Agilent Chemstation is the easiest to use but with Chemstore + DAD, the speed of retrieving data from the server is just nightmare. However for R&D purpose, it would be the best as it give you the flexibility to do basically ANYTHING real-time.
But for QC and compliance, it's not a really good idea I guess. Also you cannot line-up sequences/sample set one after anther like Chromeleon or Empower. (At least not in the version I have used 2 years ago.)
Empower is great in controlling Alliance HPLC, but it really have some problem in dealing with Agilent 1100/1200/GC. The worst thing is, when you encounter some problem and call Waters Tech support, they will say that it's Agilent's hardware problem and when you call Agilent, they will say that it's Empower's problem.
Agilent keep saying that they gave Waters the latest firmware already and they are just too slow to update their program. Our lab face glitches here and there and we still still can't get the PDA to run right and the system lost communication occationally. We are going to apply a new patch for Empower next month and lets hope it can fix most of the problem.
Simply put, I'd say use Empower with Alliance or Chemstation with Agilent. Unless your lab is really big and have multi-million dollars business deal with Waters, I don't think they would bother to
tailor Empower for differnt brands of instrument in your lab. For CFR21 Compliance, I think this is better than the other two software though.
Chromeleon is a great software. I have run Dionex IC on it for like a year and it works like a charm. However I have never used it to control other brand of instrument so I cannot give you much feedback.
Good luck!