It's not clear from the question just what behavior your program will simulate: simple combinatorial logic equations? Combinatorial and registered logic? Timing? Power requirements? Noise margins? Clock tree management?
What is a rough estimate of total no. of ICs supported in a software (free and open source Sourcforge Project Home), expected by you?
For professional design work, I expect to have a selection of 1000's of parts, and the option to extend the library with new parts as needed. Remember that every part sold by every IC vendor has some market -- some design space where it was designed to be the best IC for that purpose -- so whoever's doing the design that needs that IC is a potential user for your simulator tool, but not if the tool won't support that IC.
Obviously students might be better served by a much narrower selection, corresponding to what they've learned about in class (but also, different courses will cover different material).
Name some specific, IC (essential/recommended)
For simple logic designs, I'd include all of the basic gates (and, or, nand, nor, xor, xnor), basic flip-flops (D, T, JK), plus common higher functions (mux, demux, shift register, counter, ram, ALU, ...)
Going beyond discrete gates, you would extend your audience a great deal if you would include the equivalent functions as they're implemented in various CPLDs and FPGAs.
Also, remember for most circuits using flip-flops you'll need to have some kind of clock source available. Many systems will need multiple clocks, and designers of those
Are digital IC alone able to model a large no. of circuit, or analog elements are required along?
Your users will certainly need some kind of clock source circuit. PLL clock management circuits are also very important in many digital systems.
To simulate circuits using open-drain wired-AND logic you will need to include pull-up resistors of arbitrary values, and (to simulate timing) different capacitive loads.
To simulate circuit timing, it would be very helpful to have components representing transmission line delays between chips, as well as the effects of (parasitic or intentional) capacitive loads.
Is is correct to name IC with same function (like XOR) but different packages (like W, N, D etc.), different types (like LS, S), different manufacturers as a single name (like IC 7486)
IC 7400 & IC 7401 do same job, so is it ok if i skip 7401
To answer 4 & 5 together, it really depends on your goals. To just simulate logical functionality, you could either skip some ICs or packages, or just make one model be usable with multiple names.
If you want the pin numbers in the drawing in your program to match what the user will lay out on a breadboard or PCB, you will need to have different drawing symbols for different packages and maybe for different manufacturers (I seem to recall that back in the day Motorola had a 74xx logic series that was totally functionally compatible but used totally different pin assignments, for example).
If you include timing behavior, you will want each chip to have its distinct propagation delay, rise and fall time, setup and hold times, etc.