drathro: I hadn't considered the lack of a number pad, Colonization certainly uses one so thank you for pointing that out.
In that case,
Click-n-Type might be the on-screen keyboard of choice. Its layout is completely configurable, and it comes with a handful of pre-designed layouts, one of them containing a number pad. I just checked it with GOG's version of Colonization, and it worked. The number pad keys were recognized, as were all others.
Click-n-Type also allows users to configure their own keyboards (though that apparently requires an additional download of some third party software). But in theory, for games that use just a handful of keys, you could design your own specific keyboard layout for that game, with short distances between the necessary keys, and no unnecessary keys.
drathro: My disability allows me to hold a mouse (only just) and click the left button with my one good finger, anything else is a major chore.
Hmm. Would foot-controlled or speech-controlled input improve accessibility for you?
There are lots of different solutions available (though many are, unfortunately, rather expensive). You can check this page for a good overview of alternative input options for all kinds of disabilities:
JAN Alternative Input Devices. JAN is a US government agency that (among other things) provides technological advice to keep disabled citizens in employment. The page was written by a physician and has lots of links to other overviews, companies, and individual products. It's a very good starting point to see what's available.
If the finger is the only workable option, the perhaps check some software that lets you input morse code with the mouse button, and translates that into simulated keypresses. I haven't checked or used such programs myself though, just read that they exist. Whether that's a better solution than an on-screen keyboard depends on how difficult it is to move the mouse.
Give me an hour or so to check Pharaoh (the other game you mentioned). I just bought it in the promo and I don't think it provides a windowed mode out of the box, I'll see if there's a way to make it work with an onscreen keyboard.