Knights of the Old Republic 1 and 2 (not the MMORPG) used a "reversed engineered" version of WOTC first d20 Star Wars rules. Legally speaking, they took the 3.0 open game license and made their own version for their Star Wars licensed material but it is obvious they were taking notes from the WOTC Star Wars rulesbooks. The first one was awesome, the second was good. They both put the Old Republic MMORPG (which invented its own non-d20 ruleset) to shame.
Neverwinter Nights 1 was one of the top 10 best video games of all time but used 3.0 rules. Theoretically, you could build your own module and script in 3.5/Pathfinder rules. Some of the community made modules were just brilliant.
Neverwinter Nights 2 used mostly 3.5 (with some modified rules) but was not made by Bioware so was not as good as the predecessor. Getting the complete version with all expansions, bug fixes, and community made content still make it a pretty good and entertaining game that's worth getting from the GOG.com website. Like the 1st one, some of the community-made modules were great.
IceBlink is a RPG engine with which some people have made 3.5-ish adventures. Quality is highly variable.
Dungeons & Dragons Online uses a highly modified version of 3.5 for their MMORPG. It was OK but I got tired of the constant pressure to make "micro payments" to keep playing.
Neverwinter Online is another MMORPG but the rules are more a 3.5/4th ed fusion with some custom changes. It is somewhat fun but still not as good Neverwinter Nights.
The Temple of Elemental Evil was 3.5 but it was riddled with bugs when it came out and got bad reviews. I've heard it is decent once the patch is installed.
Dragonshard only nominally was 3.5 as you very rarely saw much of the rules at all. I've heard it is worth $5 if you find it on sale.
Unfortunately, Pathfinder Online chose not to even use the Pathfinder rules and has been a solid disappointment. Not even worth your time.