The choice of textures in your doom map is art! You have to consider hundreds of different factors if you skin your map. Color, Style, Transition, Material and Surface to mention the most important! It's easy to create a little cave out of different brown rock variants and to create a UAC base by just using silver textures but it's a real challenge to combine hellish flesh and bones with industrial metal and rusty engines.
Everything is possible as long as the Style of textures is almost the same (for example "Hexen & Doom 2" or "Quake & GothicDM" can be mixed, but never mix "Chex Quest & Strife" or "Blake Stone & Ogros"). If you have problems of finding matching color shemes, Google This!
If you start to work on maps with a totally new theme, you will come to a certain point, where one texture won't fit to another texture or floor (or vice versa) and the Transition from one Material to another might look to abrupt. This is when we start to use the power of sector borders again, with textures that fit to the overall theme (SUPPORTx textures, METALx and other textures that seem to support the architecture fit quite well). Shot 1 shows a good example (although the choice of textures/colors totally sucks) how drastic texture changes and clashes can be reduced!
The big problem a mapper always has are texture clashes of any type, wether the materials from one to another structure are similar or not, often where floor textures and wall textures meet on an edge. Take a look at Shot 2 (upper version) where all the brick stones are quite the same material but the transition seems too hard and looks not really realistic. Compare this upper version with the one below to see how to solve this with a simple extra sector!
The last thing to mention here is the importance about texture alignment. Map editors like Doom Builder and SLADE (and maybe even some more) inlcude a feature called "Auto Align Textures" and I recommend using that. Nothing looks as crappy as unaligned textures and these totally destroy the realism of you map so spend a lot of time by fixing misalignments!
Summary: "Reduce texture clashes and drastich texture changes with sector borders!"