I'm looking for prestige classes from D&D 3e or 3.5e that have a class feature of providing "+1 level of existing class features". I currently know of Uncanny Trickster (CS) and Legacy Champion (WoL). Are there any more?
I believe there not to be.
I have searched through all of my books (I own all 3.0/3.5 books, except for the dungeon-tile publications, all of my magazines (Dragon and Dungeon) dating from TSR to Paizo, and several Mongoose and Sword and Sorcery publishing books.
Those are literally the only two examples I could find as well. I even used three differen't search engines, Bing, Google, and Yahoo, and only found those two examples.
If there are other 3rd party material that has a similar prestige class special ability, I will stand corrected. But I strongly do believe, those are the only two prestige classes available outside of homebrew.
I have found a racial Paragon Class at dandwiki.com called the Aasimar Paragon class and it has your "+1 to existing class features", class feature. That's not really a prestige class though... The Factotum at level 20 can assume a class feature from up to three different base classes with his inspiration points, still not a prestige class... As you have already stated the Uncanny trickster and Legacy Champion are two prestige classes that have this class feature to them.
But don't worry I have hope!
Under the Dungeon masters guide II page 203 their is an entire section on DESIGNING PRESTIGE CLASSES!!
Upon which you could construct using that guideline any and all further modifications to your game or bring said prestige class to your GM and ask his approval to add it to his world.