FastQC is good for both pre- and post- alignment QC. Picard tools has a bunch of QC related tools you can use. For starters, I'd first look at the % of uniquely mapped reads to get a general idea of how well your sequences aligned to the reference. For human cell lines, a good alignment will be 50%+. Paraffin embedded tissue or other similar preparation methods will likely have more degradation so I'd assume that the alignments might suffer a bit. QC will typically assess the sequencing quality (how well the sequencer sequenced what you gave it to sequence), and not necessarily the quality of the material you gave the sequencer to sequence.