WRT to the 3800/320MS-
I have a 3800/300TQ. I love it-it's a versatile and sensitive set-up.
With that said, I would not recommend it to a novice GC/GC-MS user.
First of all, the 3800 is a bit of an old and quirky GC. The electronic pressure regulators, in my experience, are not as good as the ones available for the HP 5890(which is a 30 year old design, and about 10 years older than the 3800). I would consider nothing short of a Varian 450 GC for use these days, but none the less there still exists the issue that parts and knowledge for servicing Varian GCs is getting thin on the ground.
The autosampler, when working, is a solid unit but in my experience is a lot more finicky than HP/Agilent units. I seem to constantly recalibrate the tower, while I've dropped 30 year old HP7673 towers onto 5890s and had them work perfectly without doing any sort of calibration(in fact you have to dig to find calibration procedures for the HP/Agilent because it goes off so rarely). A lot of this is a function of design-the Agilent tower is stationary and sample vials are brought to it, while the Varian tower both rotates and moves up and down. I only lose HP/Agilent syringes when the plunger gums up, while the Varian seems to eat them constantly whether it's from not retracting full out of the vial before retracting, or missing the injection port, or a variety of other things. Varian syringes are getting a bit thin on the ground these days-you need a "button head" syringe with a ~2" long conical needle(similar to a hand injection syringe, although with a different point than is usually used for hand injection). The Thermo and Shimadzu syringes use a shorter needle and are not compatible. Agilent syringes use a totally different plunger head, but there are so many HP/Agilent ASs in service that they are common and readily available from several suppliers. I have only been able to get Varian compatible syringes from Trajan, and they run me 2-3x what good Hamilton-branded Agilent compatible syringes run. I fought the Varian so much that I finally pulled it off and hand inject into the GC. If I ever put another AS on it, I'd go for a PAL-type.
The 300-series MSs are a well executed and sensitive design with some very nice features to increase sensitivity. Even though mine is a triple quad, I run it as a single quad a lot and still find it somewhat more sensitive than my Agilent 5975. In my experience, though(and others have echoed this) one of the biggest downsides is that the tiny ion volumes(which I suspect contribute to its sensitivity) get dirty VERY fast and need regular cleaning to the point that it's a good idea to have a couple of them. As long as you have the proper tool, you can change volumes without breaking vacuum. Be advised, though, that the 300 series needs a different tool than the older 1200 series-someone on here very generously gave me a spare 1200 series tool and a few ion volumes. The machinist at my university was able to make a 300 series extract/removal tool and the vacuum interlock using the 1200 tool and some other parts as a reference. In short, though, I'd advise avoiding if you don't get an ion volume insert/removal tool with the instrument, as cleaning/changing otherwise involves venting, removing the glass cover, and then pumping it back down.
That's not even touching on the software, which is wonderful and versatile IF and only if you have a fundamental understanding of how mass spectrometers work. If you lack that, however, you'll be looking at a a series of confounding Excel-like spreadsheets to set up the instrument, and a lot of readily accessible options that normally shouldn't be changed without a good reason(Agilent "hides" a lot of those like filament voltage and current-they can be changed on an Agilent, but only if you go looking for them, while they are in front of you on the Varian).
I've been quoted around $45K for a refurbished basic model Agilent 7850/5975, which is a robust and reliable instrument that's also very capable. A refurbished 7850 or 7890 FID would serve you well, and will be much simpler to use.
