There is no right answer here. It's part preference, part performance. You could have 1000 very small files with < 300 lines or 100 larger files with 3000 lines. No difference, except in performance. Opening and merging 1000 files in real-time in a language like PHP is going to be slower than opening and merging 100 files.
A good IDE can mitigate this problem altogether. For example, in my IDE, I can see the methods in a separate pane, so navigating to the method I want is a breeze. Also, a decent IDE can let you jump to the source in some fashion by highlighting the method you want and pressing a key.
I think what matters more is what those files contain, now how many lines are in them.