Timing Constraints
There are several settings in ISE where you can change the effort level in the design. This will make the FPGA build times much longer, but it gives it a better chance on making your timing requirements because it causes the tools to try harder. If that does not work, then you need to review the signals that are not making timing and either re-write the logic to be faster, or relax the timing constraints on those nets.
How do you make the logic faster? The primary way is to add pipelining stages. These are flip-flops that break large combinatorial sections in to smaller chunks that the place and route with less prop delay.
Why would you relax timing constraints? Because some signals will not change on every 100MHZ clock edge. If a signal is coming from an external source which updates only every three or four 100MHZ clocks, then the signal cannot propagate through the FPGA any faster than that. The ISE tool has no way of knowing the speed of the external signals and therefore assumes the 100MHZ worst case. The way you tell ISE about this is by placing specific relaxed timing constraints on those signals.