It's a good day in my world when my favourite game, Sturmovik, fully works on Linux under Wine, and better, more reliably and at least as fast as on Windoof.
That also includes the TrackIR, thanks to these guys and their Linux-Track project - which is still a bit rough in places but generally works fine with a variety of hardware (from webcams to TrackIRs).
In addition to the Linux-track stuff you'll also want the Linux-Track WINE plugin which presents Windoof apps with a TrackIR-compatible API. That thing was a pain to get running, and you might want to check out this patch by me to make it work properly with recent Linux-Track revisions.
Apart from those: no real problems after some initial conf.ini tinkering; no more inexplicable stuttering under Windoof, no more dualbooting and smooth performance with graphics options close to the top levels.