Since reindexing request long term of running in our webserver. I thing it is better to do this one the console, to liminated the posoble timeout error.
Below are some possible command you can use.
Index product attributes for layered navigation building
php shell/indexer.php -reindex catalog_product_attribute
Rebuild Catalog product fulltext search index
php shell/indexer.php -reindex catalogsearch_fulltext
Reorganize EAV product structure to flat structure
php shell/indexer.php -reindex catalog_category_flat
Index Product Stock Status
php shell/indexer.php -reindex cataloginventory_stock
Indexed category/products association
php shell/indexer.php -reindex catalog_category_product
Index product prices
php shell/indexer.php -reindex catalog_product_price
Rebuild Tag aggregation data
php shell/indexer.php -reindex tag_summary
Index product and categories URL rewrites
php shell/indexer.php -reindex catalog_url
If you want to reindex all.
php shell/indexer.php -reindexall
Also, for other useful command parameter you can use help screen that is accessable via SSH using the command:
php ./shell/indexer.php -help
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