I think the confusion is based on the fact you titled this thread "need help, my server is slow", then someone mentioned it loaded fast to them, and you replied that you knew your server wasn't slow.
So, you should probably try to make a topic subject more related to the actual issue, since it is afterall.. the Topic.
As far as your MySQL woes, a lost connection to MySQL error means that the program (in this case, a php program called SMF) had a connection to your MySQL server, but it was closed before or during a transaction. The issue depends on how your host is configured. Some hosts run the HTTP Services and MySQL Services on the same server. If that is the case, your server is probably overloaded. If your host has a seperate MySQL server, then either the MySQL server you are accessing (and probably many other HTTP Servers at the host are accessing the same MySQL server) is overloaded, or the network connection between your HTTP Server, and the MySQL Server has problems or is overtaxed with accesses. Anyway you look at it, you will need to contact your Host provider and have them resolve that issue.
As far as comparing TP/SMF to MySpace or any other site, it is irrelavent. TP/SMF can perform as well as any other php/perl/python/other program out there given it is performing on the same servers and backbone. Obviously MySpace has a large server farm, and large bandwidth. If you do the same, your TP/SMF site will perform as well, if not out-perform MySpace. When you said you can't compare TP to MySpace, you were right, but for the wrong reason. It's simply because it is very unlikely that you will find someone with a TP/SMF site running on the same hardware/backbone as MySpace or other large social networking type of site.
Yes, I can imagine one of my scripts running on 10,000 profiles - TinyPortal.net has over 13,600 members/profiles and SMF's site has over 70,600 members/profiles. So we can indeed imagine, and in fact do know what kinds of HTTP Server and MySQL Server loads there can be. Like I said, its more of a Hardware/bandwidth thing.
As far as table overhead, 90% of your overhead is probably from the sessions table. This is normal, as sessions tables generally are the most overhead. While 40k is not extremely significant, it is certainly more than you probably would get on a normal basis for your site due to the server issues you are having I would surmise. Fixing your server issues, will most likely drop your overhead as well.