yama's yz250f (for mx) and wr250f (for trails) are the way to go. great suspenders, light weight, fantastic power, and super agility. the primary difference (besides the obvious headlight/tailight) is that the wrf has a lower first gear and higher 4th and 5th gears than the yzf. so you can crawl along in the knarly rocks in the wr's 1st gear, and then in the open (4th and 5th) it will be faster than the yzf. but for mx, the yzf's close ratios keep you way up in the powerband. and the yzf is designed to be a "big air" bike. so just figure out what you are going to do more of then lean towards either the yzf or wrf.
the crf450 and cr125 are not "roughly comparable". the crf will have much more power and the traction from the 4stroke will allow it hook up much better. so coming out of the turns you'll be going *a lot* faster once you get used to the ride. the xr400 is a completely different animal than the crf450; the xr is an older design especially suited for long desert rides, and the crf is honda's entry into the 4stroke mx racebike scene. also the xr is known to be super reliable, while the crf is new and unproven.
if you go from a cr125 to a yz426f or crf450, you should know that the words "scary fast" are going become part of your daily vocabulary. especially in tight trails. the tighter your trails are, the more nimble the bike you want. 426 or 450cc's is a bit much for the tight stuff, just too much to throw around, and they will tire you out. that's why kdx200/220's are so fast in the right hands-- good power and great agility. the klx300 is also a truly effective woods bike, but the design (esp. the suspension) is a bit dated. reliable though. so in my opinion, the best go-fast 4stroke trail bikes currently are the yama yz/wr250f and the midrange ktm's. there's rumour of a 250cc ktm 4stroke but who know's when it will show.
the wrooster
'01 wr250f
(160 miles so far and i'm averaging a crash per 20 miles...)