Always Backup your store files and database before starting upgarde.
I just upgraded my magento to 1.6. Following are the issues i faced while upgrading:
1) First of all i tried to upgarde magento using magento connect manager, but id didn\’t work as for most of modules were skipped by connect manager with message no upgrade available or dependency errors.
2) After that i try to upgrade it by downloading complete 1.6 package from magentocommerce.com and upload all the files to my magento (website) directory through FTP client.
3) After all files were uplaoded, i run my website again from browser, but it did not work and i got some server timeout errors, so i fixed timeout errors by editing by nginx conf file.
4) After inreasing timeout in server conf file, i restarted the upgarde by again accessing my website url from browser.
5) This time, i get some mysql errors after approx. 1 hour and upgrade did n\’t work.
6) So, i dropped my magento database and restored it back from my dump which was taken before starting upgrade .
7) After restoring my shop data, i again started upgarde by accessing my website from browser, this time it took a long time (approx. 10 hours), for approx. 8 hours page kept on loading, so i did not stop/close my browser window assuming that my upgarde is going on.
8) After approx . 8 hours, upgrade was still not completes, but i tried to open my website in another browser and it worked, my store was sucessfully upgarded to 1.6.
9) I tested whole site after this, and everything is working fine. Hurray.
Hope this will help someone struggling with upgarde.
W3sols Team (w3sols.com)
We customize magento community edition