There have been increasing developments in the area of wireless communications based on orthogonal frequency division multiplexing (OFDM). These standards are widely used for their resilience to frequency selective fading and inter symbol interference. OFDM derives this ability through dividing the overall frequency spectrum into smaller narrowband carriers which undergoes manageable and correctable fading through the wireless channel. With the increasing demand to maximize the use of the wireless spectrum both efficiently and securely, there has been significant research in the areas of cognitive, adaptive and secure wireless communication techniques across all the layers of the protocol stack. This dissertation mainly focuses the research developments targeting the physical or baseband layer. Research in these areas that are purely based on software implementations solutions benefit from faster development and turn around times but lack the ability to be tested and validated in real time scenarios as is possible with hardware based solutions. Thus an ideal implementation would be one that incorporates the flexibility offered by software and the real time speed offered by hardware. The flow of data within hardware-implemented baseband kernels is inherently predictable for all communication standards, which helps designers build fast, synchronized and optimized baseband kernels on FPGAs. However off-the-shelf FPGA based SDR architectures often strongly adhere to the few specific standards they are built for and thus are hard to change (in terms of coding rates, modulation, and subcarrier sizes) without substantial effort due to synchronization and data-rate issues. In this dissertation, we develop a programmable and flexible hardware implementation of the physical layer across wireless communication systems that use OFDM techniques. We have developed an OFDM pipeline comprising of all generic physical layer stages in which each stage can be configured at design time or at run time to accommodate different standards as well as different configuration settings within a standard. This flexibility is achieved by designing the overall pipeline to be insensitive to the latencies incurred by individual stages using the concept of state-aware stalling functionality and also with the use of infused control data for shepherding payload across the pipeline. Such a pipeline can be easily used as a research platform to experiment with different OFDM standards as well as for rapid prototyping purposes. The overall system and its performance is characterized in terms of functional correctness, area cost of implementation and flexibility. Experimental and simulation results are obtained and analyzed for the IEEE 802.16 WiMAX and 802.11a/n standards under different coding rates (1/2 and 3/4), modulation schemes (4QAM and 16QAM), and symbol sizes (128 and 64 sub-carriers), all within a common framework that does not require re-synthesis or recompilation because of the inherent capability to perform packet by packet reconfiguration. We also show results on how the flexibility built into the architecture makes it possible to implement non-contiguous OFDM (NC-OFDM) which enables the utilization of sub-carriers efficiently around noisy frequency bands by nulling and avoiding those bands while data is loaded. Keeping the ever growing relevance of cognitive radio research in view, we also built our system to also be flexible in settings user defined inter-packet and inter-frame spacing which comes into prominence in research dealing with adaptive modulation and re-configurable antennas. To further solidify the advantages of the system we built over other platforms we describe two physical layer security techniques that we built that no other hardware based testbeds currently available can implement without significant implementation effort. The first application utilizes the flexibility built into the testbed's packet organization and packet detection modules to be able to modify the wireless packet preamble enabling wireless transmissions between intended parties to go undetected to intruders. The second application utilizes the flexibility built into the interleaver module enabling it to interleave and de-interleave data based on secret keys known only to the intended communicating parties preventing intruders from decoding packets.