As delivered stock, the US model Yamaha WR250F (but not the Canadian model) has a throttle-stop screw which prevents the throttle slide from opening more than about 3/4 of the way. Why this is, I don't know. Perhaps it serves to keep the noise level down, or make it more likely you won't over-rev the engine during break-in. Maybe it's an EPA thing. Whatever.
If you modify the aforementioned screw, then the bike will rev like never before and you'll have a "free" power increase. You may wish to couple this modification with removal of the airbox lid, or perhaps just the "snorkle" that bolts into the lid. Some riders also remove the baffle from the exhaust, but I prefer to retain it on the assumption that loud pipes cost riding areas. My bike runs pretty damn strong with the baffle in place anyway...
You find the throttle stop screw here, on the right side of the carb, behind the big black plastic cover. To remove the cover (which probably isn't strictly necessary but makes seeing what you're doing easier), remove the 4mm allen bolt under the rubber boot. You'll have to peal the rubber boot back a bit to wiggle the cover off after removing the bolt.
The throttle stop screw is also a 4mm allen, but it's lock-tighted and requires some care in removing so as not to damage the screw. You probably won't be able to get anything other than a simple allen wrench to fit the tight space behind the shock reservoir. You may even need to hack off the end of your allen wrench a bit.
The screw has some pinkish stuff on the threads, and is shown partially removed near the center of the above picture, just below and slightly to the left of the throttle cable ends in the circular gizmo.
This is the throttle stop screw. Mine was 33mm long as stock. I removed exactly 6mm with a hacksaw, resulting in a 27mm screw. I beveled the cut end with a file to mimic the original end. This allows the throttle slide to open all the way. It makes a huge difference in performance!
To determine how much to cut off the throttle screw, I pulled the air box boot off the carb, and removed the black plastic piece it was attached to. That way I was able to see and feel the throttle slide itself as I backed out the original, unmodifed screw. You can probably avoid this step if you trust my measurements and the likelihood that Yamaha made all the carbs and throttle stop screws the same. Besides, your carb isn't likely any different than mine.
P.S. The WR400 and WR426 (US) models have similar throttle stop screws, but they also have different carbs than the 250 models. This article says that the stock 400/426 throttle stop screw is 30mm, which should be cut down to 23mm (i.e. remove 7mm). If you have more info about this that should appear here, please email me (Marc) and I'll update this page...