I've got a ThrustMaster T.Flight Stick X as well as the HOTAS X. Both are great, but I liked their predecessors better: The Top Gun Fox 2 Pro and Afterburner II HOTAS. They're both identical to the modern T.Flight versions, but they had really nice programming software that even worked in Win98SE. The T.Flight sticks still work fine in Win98SE but lack that programming software. You'll need to use something like JoyToKey or XPadder to program them if your game lacks a built-in function for button assignment. I'm not sure about assigning buttons in DOSBox, so I don't know if the lack of programming software is even an issue for you. Both are great sticks and you won't go wrong with either of them unless you're left-handed.
If you're left-handed or think you might eventually want to use the stick with your left hand (damn RSI), then consider the ThrustMaster T.1600-M as NamelessPlayer has already mentioned. I don't own one, but I'll buy one if ever see them for $20 again at Micro Center. They seem like they would be superior to the T.Flight sticks, but some reviewers complain about odd button placement and also a "cheap" feeling to them.
I've never had good luck with Logitech sticks. I haven't tried the Logitech Extreme 3D Pro, but I would avoid it based on my past experiences with other Logitech joystick products.
I've had mixed experiences with Saitek products. I tried a gameport version of the original Cyborg stick in the late 90s and didn't like it at all. I currently own an X-45 HOTAS which I like OK, but the programming software can be a bit goofy. The X-45 stick and throttle also feel a bit too big for my hands; I should have returned it and found something that fit me better. I've also got a Cyborg Evo which looks really cool, but has a mushy center position which requires me to set a larger-than-preferable deadzone. The Cyborg Evo also works well in Win98SE and includes programming software.
Whatever you buy, make sure it fits your hands or you'll get annoyed after awhile.
My personal recommendation is for you to find an old MS SideWinder Precision Pro with the USB dongle. They're cheap, work great, feel great, have optical sensors, and still work well even in Windows 7. They're also extremely durable and last a very long time. If you use them in Win9x, you can also run the SideWinder programming software. I see used ones at GoodWill all the time for $4 or less, but make sure you get the USB dongle for it or you'll be outta luck.
There's also the CH FlightStick Pro which is basic, durable, and a very good stick. It is not, however, cheap. You might be able to find one used on eBay for cheap.