I have managed to get this running by using Wineskin on Mac very well in fullscreen mode.

I want to run this in windowed mode, but am unable to adjust the size of the window despite adjusting the virtual desktop resolution within Wineskin settings.

Also when I run this in windowed mode, is there any way of allowing the mouse to leave the application window (like in the DOS emulator Boxer which allows the mouse to leave the game by using command-click).

I haven't been able to get this game into proper windowed mode either. Unfortunately it's like that with WINE, some games you can get windowed with a free mouse cursor, others you can get windowed but the mouse cursor is locked inside the game, and still others you can only get full screen, it's really hit-and-miss.

(Sometimes command-return works to switch between fullscreen and windowed modes, but not in this case)

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Also, not directly related to your question, but just in case you hadn't heard about this app, it's got a lot of pre-made WINE wrappers and even installs them for you:
http://paulthetall.com/portingkit-2/

Thanks for your reply. It helps to know it's not just me! I have indeed used porting kit before - for Thief Gold and System Shock. Quite a helpful tool. Have started fooling about a bit with creating my own wrappers. One little trick I picked up for Populous 3 actually, although you may know it - if you type "-allres" into the exe flag section within wineskin advanced settings - you get a bunch of extra resolution options including widescreen (i think i was using 1366x768 and it worked a treat)

No, I hadn't tried that. I'm actually in the middle of replaying Populous: The Beginning right now (taking a break in the middle, actually), so I'll give it a try next time I play. Thanks :)!