What kind of automatic transmission fluid does a 1993 Honda Civic use?
nothing but genuine Honda ATF.
The engine oil capacity for a 1999 Honda Civic is 3.5 quarts. (Just in case you meant transmission fluid - since you mentioned it's an automatic - the A/T fluid capacity is 3.0 quarts. Note, if you have a GX or HX model with a Continuously Variable Transmission, it will take 4.0 quarts of Honda CVT fluid).
Can any brands other than Honda transmission fluid be used in a 2000 Honda Civic EX with automatic transmission?
In general, use only Honda ATF. Any other so-called replacement, or universal fluid will cause shifting problems. Other ATF fluids can be used in a pinch, but you risk damage to the transmission. There are two types of ATF fluids for Honda's: for standard automatic tranny's, ATF-Z1. Dextron II was recommended by Honda in earlier models. Dextron III is NOT recommended. For Continuously Variable Trann's, Honda recommends CVT fluid (Civic HX, GX, & Hybrid as…
From AMSOIL.com: 1999 HONDA ACCORD 2.3L 4-cyl Engine Code F23A1 F23A4LUBRICANTS & FLUIDS: Manual Transmission,......GLS  AMSOIL Synthetic Synchromesh Transmission Fluid (5W-30) (MTFQT) Automatic Transmission,MAXA......SLF  AMSOIL Synthetic Universal Automatic Transmission Fluid (ATFQT) Automatic Transmission,BAXA......SLF  AMSOIL Synthetic Universal Automatic Transmission Fluid (ATFQT)  Honda MT fluid, Part no. 08798-9016 or equivalent  Honda ATF-Z1 Automatic Transmission Fluid, Part no. 08200-9001 or equivalent