You look at the assembly code, grab an Intel Programmer Reference manual (they were about 1000 pages), look up each instruction opcode and that would tell you the clock cycles. For memory operations it is much more difficult due to caching. However, for many hot regions of code, the data is already in the L1s so manual counting is sufficient. (At the time there was a book called The Black Art of ... Assembly? I can't recall, and I should be flogged for forgetting it... but it was directed at game programmers and covered all sorts of assembly tricks for Intel CPUs.)
Also, a little later in the 90's: VTune. When VTune dropped it was a game changer. Intel started adding performance counters to the CPUs that could be queried in real-time so you could literally see what code was missing branches or stalling, etc. Source: I worked with Blizzard (pre-WoW!) developing VTune, feeding back requirements for new performance counter requests from them and developers.