Hi, as you may know Google change their algorithm multiple times each year so here's a few things you should go over first:
- Solve internal duplicate content issues (very big deal after the Panda update)
- Find out if anyone has plagiarized your content using Copyscape (file DMCAs if you need to)
- Can the content on your homepage can be accessed via these URLs?:
www . yoursite . com/index.html
yoursite . com/index.html
www . yoursite . com/
yoursite . com/
Use 301 redirect and canonical link element to solve this issue if it exists.
- Consider using external style sheets
- Make sure your site is coded using the latest approved coding standards (old web sites usually suffer from this problem)
- Site loading time is now part of their algorithm, how long does your site take to load up a page?
From what you are describing your site doesn't seem to have been penalized but, instead the more logical things that have happened are that you have lost a few positions due to small oversights or due to matters outside of your control
a) Your competitors have made a strong push to out-rank you
b) You have lost a few valuable backlinks either because they have been removed or they have lost value for reasons outside your control.
Hope this helps, let me know if you need more help