I use the Topeak MTX system at work. It is a nice set-up that works very well. The one I have (at work) is the one that has the zip out side panniers. However, they are not waterproof, and they require the Topeak rack.

My order of preference if it was my money on my own bike:

#1- saddlebag (Carradice, due to it's durability and waterproof fabric; there are several sizes available, depending on need). I have several Carradice bags for my personal bikes. I have never had one fail on me, they perform as they should year after year. They look like new after having them for several years. They are waterproof and breatheable. I love that no cover is needed and there are no zippers to eventually fail. I expect my great-grandkids will inherit my Carradice bags in 50 years, and they'll still probably look like the bags Carradice is selling 50 years from now.

If you need a quick release option, the Carradice SQR provides that. It's probably negligible, but I also believe saddlebags are more aerodynamic as much of the bag is directly behind the thighs. For either a trunk bag or panniers, they would not be directly behind the thighs.

#2- (if you're not taking the bag on and off daily and/or require a beam rack) Arkel Tail Rider trunk bag with Arkel Randonneur Rack. This rack is the best of the beam racks, and shouldn't have any problem mounting to just about any frame. However, you can't use panniers with it, and it's a bit more expensive than many other racks. If you have to have a beam rack, this is the only option, in my opinion.

#2- (if you're taking the bag on and off daily): Topeak MTX Trunk Bag DXP and Topeak MTX rack (disc or non disc depending on what you need).

I really like the Topeak MTX bag system. It's very easy to put on and take off the bike. It holds a ton of stuff, particularly with the fold-down side panniers. However, there are two limitatios of it: 1- the side pockets hold the panniers. They are mostly filled with the panniers. If you put anything in them, when you deploy the panniers you have to re-locate anything you had already put in the side pockets. You can put very small items in the pannier and then put the pannier away in the side pocket, but then you have to deploy the pannier to re-gain access to whatever small item you stowed in the put-away pannier. I wish the panniers deployed separately from the pocket. 2- they (the MTX bag and/or deployed panniers) are not waterproof. You will need a rain cover if you ride in the rain. You'll be fine in light sprinkles without a cover, but anything more than sprinkles and a cover is necessary. It's also worth noting that the zippers seem to kink easily. I haven't had a zipper fail, but I've only been using one for about a month. I think the zippers are probably the weak link.