Need advice for addressing DBTuner suggestions

I don't know if it is the right place, but I would appreciate some help to optimize my database server.

I switch to innodb, set collation and indexes as suggested.
I adjusted my.cnf according to the initial recommendation of DBTuner and some googling.
Below is the current report.

For example, these warming do not change whatever I set for the mentioned parameters

• The query cache is not being fully utilized.
• Too many temporary tables are being written to disk. Increase max_heap_table_size and tmp_table_size.
• Too many intermediate temporary tables are being created; consider increasing sort_buffer_size (sorting), read_rnd_buffer_size (random read buffer, ie, post-sort), read_buffer_size (sequential scan).
• The rate of opening tables is high, increase table_open_cache to avoid this.

I already set huge numbers without any effect.

Note that I am using cacherouter with APC, this might have an impacr on the mysql settings.

Thanks for help ,

Queries
Uptime in seconds: 522848
Uptime: 6d 1h 14m 8s
Questions: 90973971
% slow queries: 0.00142678173299
slow query rate: 0.000235773956733 per day
Long query time: 2
Slow query logging: ON
% reads: 43.5249923387
% writes: 56.4750076613
qps: 173.996976177
reads per sec: 0.0719245237252 per day
writes per sec: 0.0933242675105 per day
Queries: 173.996976177 per second
Connections: 207 Thousand
Bytes sent: 266 Billion
Bytes received: 34 Billion


versions
Supported Version: 5
Release Series: 5.1
Minor Version: 58
Distribution: (Debian)
Distribution: (Debian)

MySQL Architecture: x86_64


Query cache
Query cache efficiency (%): 93.8692499175
% query cache used: 49.0942209959
The query cache is not being fully utilized.
    (Qcache_free_memory / query_cache_size * 100 <80)
    (527145184 / 1073741824 * 100 49.0942209959<80)
Query cache low memory prunes: 0 per day
Query cache size: 1.0 Gb
Query cache min result size: 8.0 Mb


Sorts
Total sorts: 491378
% sorts that cause temporary tables: 0.109080992637
rate of sorts that cause temporary tables: 3.6905563376 per hour
sort_buffer_size: 500.0 Kb
read_rnd_buffer_size: 256.0 Kb
Sort rows: 12.1683414683 per second
There are lots of rows being sorted. Consider using indexes in more queries to avoid sorting too often.
    (&hr_bytime(Sort_rows/Uptime_since_flush_status) =~ /second|minute/)
    (dbtuner_hr_bytime(6362193/522848) dbtuner_stristr('12.1683414683 per second', array('second', 'minute')))

Joins,scans
rate of joins without indexes: 1.27814010955 per second
There are too many joins without indexes -- this means that joins are doing full table scans.
    (&hr_bytime((Select_range_check + Select_scan + Select_full_join)/Uptime_since_flush_status) =~ /second|minute/)
    (dbtuner_hr_bytime((0 + 654239 + 14034)/522848) dbtuner_stristr('1.27814010955 per second', array('second', 'minute')))
rate of reading first index entry: 1.89994606463 per second
The rate of reading the first index entry is high; this usually indicates frequent full index scans.
    (&hr_bytime(Handler_read_first/Uptime_since_flush_status) =~ /second|minute/)
    (dbtuner_hr_bytime(993383/522848) dbtuner_stristr('1.89994606463 per second', array('second', 'minute')))
rate of reading fixed position: 6.39883675562 per second
The rate of reading data from a fixed position is high; this indicates many queries need to sort results and/or do a full table scan, including join queries that do not use indexes.
    (&hr_bytime(Handler_read_rnd/Uptime_since_flush_status) =~ /second|minute/)
    (dbtuner_hr_bytime(3345619/522848) dbtuner_stristr('6.39883675562 per second', array('second', 'minute')))
rate of reading next table row: 5629.62670795 per second
The rate of reading the next table row is high; this indicates many queries are doing full table scans.
    (&hr_bytime(Handler_read_rnd_next/Uptime_since_flush_status) =~ /second|minute/)
    (dbtuner_hr_bytime(2943439065/522848) dbtuner_stristr('5629.62670795 per second', array('second', 'minute')))

temp tables
tmp_table_size-max_heap_table_size: 0
tmp_table_size: 1.0 Gb
max_heap_table_size: 1.0 Gb
% temp disk tables: 19.4564074878
temp disk rate: 10.9182401004 per minute
Too many temporary tables are being written to disk. Increase max_heap_table_size and tmp_table_size.
    (&hr_bytime(Created_tmp_disk_tables/Uptime_since_flush_status) =~ /second|minute/)
    (dbtuner_hr_bytime(95143/522848) dbtuner_stristr('10.9182401004 per minute', array('second', 'minute')))
temp table rate: 45.1981837934 per minute
Too many intermediate temporary tables are being created; consider increasing sort_buffer_size (sorting), read_rnd_buffer_size (random read buffer, ie, post-sort), read_buffer_size (sequential scan).
    (&hr_bytime(Created_tmp_tables/Uptime_since_flush_status) =~ /second|minute/)
    (dbtuner_hr_bytime(393863/522848) dbtuner_stristr('45.1981837934 per minute', array('second', 'minute')))


MyISAM index cache
MyISAM key buffer size: 256.0 Mb
max % MyISAM key buffer ever used: 34.4104766846
MyISAM key buffer (index cache) % used is low. You may need to decrease the size of key_buffer_size, re-examine your tables to see if indexes have been removed, or examine queries and expectations about what indexes are being used.
    ((Key_blocks_used)*key_cache_block_size/key_buffer_size * 100 <95)
    ((90205)*1024/268435456 * 100 34.4104766846<95)
% MyISAM key buffer used: 35.8875274658
MyISAM key buffer (index cache) % used is low. You may need to decrease the size of key_buffer_size, re-examine your tables to see if indexes have been removed, or examine queries and expectations about what indexes are being used.
    ((1-Key_blocks_unused*key_cache_block_size/key_buffer_size) * 100 <95)
    ((1-168067*1024/268435456) * 100 35.8875274658<95)
% index reads from memory: 99.882188626


other caches
table open cache size (5.1+): 5000
Size of the table cache
    (table_open_cache >-1)
    (5000 5000>-1)
rate of table open: 5.20659924108 per minute
The rate of opening tables is high, increase table_open_cache to avoid this.
    (&hr_bytime(Opened_tables/Uptime_since_flush_status) =~ /second|minute/)
    (dbtuner_hr_bytime(45371/522848) dbtuner_stristr('5.20659924108 per minute', array('second', 'minute')))
% open files: 60.7468477207
rate of open files: 43.1230491462 per hour
Immediate table locks %: 99.9765799932
Table lock wait rate: 22.9007283187 per hour
thread cache: 100
Total threads created: 30
thread cache hit rate %: 0.000144535126854
Threads that are slow to launch: 0
Slow launch time: 2


Connections
% connections used: 10
Max connections used: 30
Max connections limit: 300
% aborted connections: 0.0274616741022
rate of aborted connections: 9.41918110043 per day
% aborted clients: 0.0284252416146
rate of aborted clients: 9.74967868291 per day


InnoDB
Is InnoDB enabled?: YES
% innoDB log size: 13.0208333333
InnoDB log file size is not an appropriate size, in relation to the InnoDB buffer pool. Consider changing either\ninnodb_log_file_size or innodb_buffer_pool_size
    (innodb_log_file_size / innodb_buffer_pool_size * 100 >=0)
    (838860800 / 6442450944 * 100 13.0208333333>=0)


other
MyISAM concurrent inserts: 1

INSERT DELAYED USAGE

Delayed_errors 0

Delayed_insert_threads 0

Delayed_writes 0

Not_flushed_delayed_rows