Like many people running Linux I also have a Thinkpad (T400). It works okay, but it still has some significant issues. The specific things I have problems with:
* Sleep; unlike some previous experiences the laptop does pretty reliably come back after sleep, but it's slow to wake up and the experience feels crude. The locked screen login screen for instance requires a keypress, and then another second before you can actually enter the password making it easy to leave out the first character of your password. I'd remove it entirely but I can't find a preference for that.
* Automatic sleep via closing the screen is a pain, primarily because of the slowness. If you regret having closed the laptop (i.e., you forgot just one thing) then you open it up only to see it pokily trying to sleep, waiting, and trying to wake it up. I've resorted to turning off all automatic sleeping, which also causes lots of problems but at least is predictable.
* External monitors work great now, they've finally figured that out (at least with the video hardware in a Thinkpad; though it seems generally good these days). Still it's tweaky and annoying. I run a lot with two monitors, and everytime I reconnect I have to tweak the settings and go through a little dance to avoid bugs in screen layout (connect monitor, orientation is wrong, mirror screens, apply, unmirror, rearrange, fix resolutions, apply). With my previous Dell laptop I had to logout to connect a screen, so at least it's better.
* Sometimes when I go into suspend it fails. So I'll tuck my laptop away, not wanting to wait 20 seconds to see if it successfully slept, and then later realize my backpack is hot because it's running full speed in there.
* Battery life is poor. One cool feature of Thinkpads is you can remove the DVD drive and replace it with a battery. This takes a long time to charge, but it's cool (and hotswapping works great, in case I want the DVD drive). Still I only get a couple hours of battery life. When I've tried to apply tweaks to improve battery life I've broken things or disabled hardware.
* Wireless is not reliable in more complex setups, e.g., sometimes WPA doesn't work.
* Sometimes wireless doesn't come back after going into airplane mode.
* The hardware has good and bad parts. The physical build quality is unimpressive. The dock is nice, and only available with a couple kinds of laptops (Thinkpad, Dell... not sure what else?) The speakers are passable, about the same as a Macbook. You don't need a dongle for a VGA monitor, but you need a dock to do DVI. It's not terribly hot. The Mac screens are definitely better. I like the mouse nipple, but the touchpad on a Mac is way better than the Thinkpad's touchpad. Three mouse buttons, very nice for Linux. The camera works, video chat works, bluetooth works, and probably a bunch of other things that wouldn't be givens a few years ago on Linux.
I would seriously consider a laptop specifically designed for Linux (like System76; someone tweeted me another one a while ago but stupid Twitter doesn't let me look back to old replies). But it feels weird because I've never known someone who personally has such a laptop. And it's very hard to trust someone who says "Linux works great on X" because there are a lot of people who have a very low standard of what "great" means.