Alcatel-Lucent won a lawsuit against MS in 2008 on a patent for audio file playback. That was later overruled by a higher court.
Bristol Technology attacked MS for not revealing needed Windows sources and entering other markets. MS was charged to pay $1M to Bristol in 2000.
Spyglass, the company that originally built what is Internet Explorer today, filed a case against MS on the basis that MS was giving their product away for free after they licensed it from them, inhibiting them from making any money and won $8M (which I would consider a ridiculously low sum today - apparently, internet wasn't considered important by that court at that time).
Stac was already mentioned in another answer
Sun Microsystems were successful in court in forcing MS stop shipping their own "MS standard" Java VM, probably the only company that successfully attacked MS's traditional way of working with open industry standards (pretend to adopt, change in an incompatible way, take over, make your own version).
There were numerous lawsuits other than that in MS history, obviously. MS policy has apparently always been to settle such lawsuits in private agreements outside court.
Most of those (except the first, which MS won in the long run) were not directly on theft of IP, but rather improper usage of IP or "predatory business practices". I personally think IP theft is so hard to prove, (especially has been in the early days, and see SCO vs. Linux) that lawyers will likely revert to other means to get at someone if they can. Most of the accusals of IP theft MS decided to settle outside court, probably to cover the details.