I can't comment on Varian vs. PE. The Varian LC systems are not good, but I hear the GC systems are good. We have had a terrible experience with the Varian Galaxie software, but I have heard reports from GC users that it is not as bad for controlling GCs. I feel that the manufacturer assertation that the Galaxie software is 21 CFR part 11 compliant to be a gross exaggeration, however, and I feel the design is cumbersome and above all very fragile.
If you are considering the Varian, take a cold, hard look at the software if you are required to purchase Galaxie with it. In particular, consider the impact of the fact that the instance window itself runs the instrument and that there is no way to change the logged in user of the instance window, so that actions taken on a particular run cannot be tracked on a per-user basis, and your run is lost if the instance window must be closed, for example due to one of Galaxie's frequent crashes. If this type of audit trail is important to you, then I feel you should avoid Galaxie.
I do have experience with the Agilent G1888A connected to an Agilent 6890 either via a needle into the split/splitless inlet with manual pressure control, or the manufacturer-recommended splicing of the transfer line into the carrier line of the split/splitless inlet with electronic pressure control. The more I use it, the more I don't like the G1888. I find it very fussy and problem-prone. The manufacturer-recommended configuration is terrible, with vapors passing through bare stainless steel through a cool zone that you have to mitigate yourself.
I think the G1888 would be better if connected to the 6890 via the Agilent volatiles inlet, but overall I am not a huge fan of the Agilent equipment. Of the GCs I have tried the one I liked the best was actually an old Shimadzu, and I would be very favourably disposed towards checking them out for new purchases.