There is a few differences. Here is the sql generated for anonymous users for the articles on the homepage from index.php:
Text Formatted Code
SELECT s.*, UNIX_TIMESTAMP(s.date) AS unixdate, UNIX_TIMESTAMP(s.expire) as expireunix, u.uid, u.username, u.fullname, u.photo
FROM gl_stories AS s, gl_topic_assignments AS ta, gl_users AS u, gl_topics AS t
WHERE (s.uid = u.uid) AND (ta.tid = t.tid) AND ta.type = 'article' AND ta.id = s.sid AND (date <= NOW()) AND (draft_flag = 0) AND frontpage = 1 AND ta.tdefault = 1 AND (s.perm_anon >= 2) AND (ta.tid IN ('General','Geeklog'))
GROUP BY s.sid, s.uid, s.draft_flag, s.date, s.modified, s.title, s.page_title, s.introtext, s.bodytext, s.text_version, s.hits, s.numemails, s.comments, s.comment_expire, s.trackbacks, s.related, s.featured, s.show_topic_icon, s.commentcode, s.structured_data_type, s.trackbackcode, s.statuscode, s.expire, s.postmode, s.advanced_editor_mode, s.frontpage, s.meta_description, s.meta_keywords, s.cache_time, s.owner_id, s.group_id, s.perm_owner, s.perm_group, s.perm_members, s.perm_anon, expireunix, u.uid, u.username, u.fullname, u.photo, date
ORDER BY featured DESC, date DESC LIMIT 0, 6
It may be a bit easier to follow but here is the sql from lib-common.php used by the function COM_whatsNewBlock to create the list of articles for the What's New Block.
Text Formatted Code
SELECT sid, title
FROM gl_stories, gl_topic_assignments ta
WHERE (date >= (date_sub(NOW(), INTERVAL 86400 SECOND))) AND (date <= NOW()) AND (draft_flag = 0) AND ta.type = 'article' AND ta.id = sid AND (perm_anon >= 2) AND (ta.tid IN ('General','Geeklog'))
GROUP BY sid, title, date
ORDER BY date DESC
Remember the sql statement for this does depend on what topics the user (which is anonymous on my Development Server) has access to. You also could have articles belong to multiple topics (which is the reason why you need the group by clause).
The main thing to speed up things that you might be missing are indexes on the SQL tables in your database. Take a look at the sql tables involved in the sql statements and then take a look at the creation of those tables in mysql_tableanddata.php file. Indexes on tables can make a HUGE difference in speed.
One of the Geeklog Core Developers.