This is of particular interest to me, because my next map will certainly require a custom engine; at least one with increased capacity, and preferably one with skybox support and tga sprite replacement textures.

I'd like to get a good idea of what engines most people here find acceptable. 

standard glquake properly on my setup, dont know why.

Instead I use mhquake with all 'enhancements' turned off except for model interpolation. So it looks and runs exactly like glquake would but with smoother animation.

For levels like nesp09 which need higher edict counts, I use the nehahra version of darkplaces.

Fitzquake would be my preferred engine if it had model interpolation and was capable of handling levels like nesp09. The software emulated lighting it can do is wonderful.

As for darkplaces, I liked earlier versions but havent tried it lately because I ran into big problems with it when bumpmapping was introduced, mainly due to lack of documentation to turn off stuff. 

For my part I'm currently mapping using FitzQuake 0.75 as a "Quake test" engine (it support colored lightning, transparent water, for example, and have a better capacity ,in term of resolution and performances than a standard WinQuake for example)
Furthermore I suppose this is the most used engine by many of us here... let me know if I'm wrong !!

Regarding custom Quake engine, I don't know if an engine like the one you required exists today... Many custom engine features are really specific to a map (or pack) and thus are developed especially for a precise project...
If you want a special custoom engine, I think you'd rather modify existing Quake C code by yourself.. or be helped by a good software "Quake" engineer ;P 

seems good, but it won't load my current map, which exceeds a number of limits. 

Yes, darkplaces used to be very nice, but as more and more features were added, it just moved further and further from quake. It's not really a glquake replacement anymore - OK I guess if you are making a completely new TC, but that's narrowing the user base a bit IMO. 

Your latest map seems to be a very huge map if FitzQuake is not able to load it !! BTW, what are the number of limits you exceed ?? 

Fitzquake would be my preferred engine if it had model interpolation and was capable of handling levels like nesp09. The software emulated lighting it can do is wonderful.

You realise that the software-emulated lighting was first written by LordHavoc for Darkplaces and that other Quake engines are mostly using parts of his code to archieve the same? :) 

Well, just edict limits really. Static entities, that sort of thing. Also, unless it has a higher tolerance for packet overflows, I'm sure it would cause chokeage in the final battle(s) too.