I think I can get about 4 lines - RTS,CTS,DTR,DSR

Yes, RTS and DTR are output and CTS + DSR are inputs to the PC.

can I use the secondary RTS, CTS etc of the 25 pin version. If so how many are available to me ? And whether all 25 pin serial ports support these ?

You can use them. As said above, 2 are inputs and 2 are outputs and to the best of my knowledge, all these 4 signals are available on all standard PC connectors whether 9 pin or 25 pin. However, pin assignment varies.

I have been using DTR and DSR (the outputs) to powert he PC side of my optically isolated RS-232 to TTL converter (to interface my projects to PC) for years and never faced any problem. However, the power which can be drawan out of thee pins, vary from PC to PC (depending upon line drivers/receivers used inside).