On a fresh 2.0.0 installation using only builtin templates (SNMP devices), I frequently get messages like these in /tmp/zabbix_server.log :
11858:20120621:173328.785 [Z3005] query failed: [1205] Lock wait timeout exceeded; try restarting transaction [update items set lastclock=1340292671,lastns=654346890,prevvalue=lastvalue,lastvalue='ET-WLB01' where itemid=23471;
11859:20120621:173457.775 [Z3005] query failed: [1205] Lock wait timeout exceeded; try restarting transaction [update items set lastclock=1340290488,lastns=545936090,prevvalue=lastvalue,lastvalue='30.000000' where itemid=23328;

Even more often: 11787:20120621:173328.800 slow query: 104.092488 sec, "update items set name='Free inodes on $1 (percentage)',key_='vfs.fs.inode[/,pfree]',type=0,value_type=0,data_type=0,delay=60,delay_flex='',history=7,trends=365,trapper_hosts='',units='%',multiplier=0,delta=0,formula='1',logtimefmt='',valuemapid=null,params='',ipmi_sensor='',snmp_community='',snmp_oid='',port='',snmpv3_securityname='',snmpv3_securitylevel=0,snmpv3_authpassphrase='',snmpv3_privpassphrase='',authtype=0,username='',password='',publickey='',privatekey='',description='',interfaceid=7,flags=4 where itemid=23696;
update item_discovery set key_='vfs.fs.inode[

,pfree]',lastcheck=1340292704,ts_delete=0 where itemid=23696 and parent_itemid=23507;

All devices were added using Discovery on a few subnets, adding and linking to SNMP Device template anything that responds. Currently 271 devices are added.
(Note: I also disabled everything except IfAlias, which is updated only once pr. day to lower traffic )

Zabbix server runs on a VM, with 6 2,5Ghz Xeon cores and 2GB memory.
MySQL runs on dedicated iron with 8 2,5Ghz Xeon cores and 8GB memory, with /varrlib/mysql mounted on a 4-disk RAID5 volume consisting of 10k RPM SAS disks.
That should be able to do some damage, but I'm seeing close to 2k QPS on MySQL on average.

Attaching slow query log, zabbix_server.conf and my.cnf.