In my current campaign, I've used a lot of wererats. Rather than deal with a template, I made a new critter as the base wererat and then slap levels on it for tougher versions. I also don't want the hassles of lycanthropy, so I just cut it out as a communicable disease. IMC, werecreatures are separate races, not cursed or diseased individuals.
Wererat CR 2
Usually NE Medium Monstrous Humanoid (shapechanger)
Init +3; Senses darkvision 60 ft., scent, low-light vision; Listen +6, Spot +7
Languages Common
AC 17, touch 13, flat-footed 14
hp 22 (4 HD); fast healing 5
Fort +2, Ref +7, Will +5
Weakness silver vulnerability
Speed 30 ft. (6 squares); climb 20 ft.
Melee short sword +7 (1d6+1) and
bite +5 (1d4)
Ranged sling +7 (1d4+1)
Space 5 ft; Reach 5 ft.
Base Atk +4; Grp +5
Atk Options sneak attack +1d6
Abilities Str 12, Dex 16, Con 13, Int 11, Wis 13, Cha 12
Feats Multiattack, Weapon Finesse
Skills: Balance +5, Bluff +7, Diplomacy +3, Disguise +7 (+9 acting), Escape Artist +9, Hide +9, Intimidate +3, Jump +3, Listen +7, Move Silently +9, Spot +7, Tumble +9, Use Rope +3
Possessions: Short sword, sling, 10 bullets, leather armor
Alternate Forms (Ex): A wererat can take the form of a human, a rat-human hybrid, or a rat. In human form, it has the special ability of looking like a normal person. In hybrid form, it gains a climb speed and a bite attack. In rat form, it becomes size Tiny. It can't attack, but it gains a +20 bonus to speed. To keep things simple, its gear shifts with it. Shifting form is a swift action that the wererat can perform once per round.
Silver Vulnerability (Ex): The wererat's fast healing does not apply to damage from silver weapons.
Trust Me (Ex): Anyone attempting to use a spell or ability that detects alignment must make a Sense Motive check opposed by the wererat's Bluff. On a failed check, the wererat detects as neutral.
Wererat Rogue CR 4
Usually NE Medium Monstrous Humanoid (shapechanger)
Init +5; Senses darkvision 60 ft., scent, low-light vision; Listen +6, Spot +7
Languages Common
AC 19, touch 15, flat-footed 14
hp 36 (6 HD); fast healing 5
Fort +4, Ref +10, Will +7
Evasion
Weakness silver vulnerability
Speed 30 ft. (6 squares); climb 20 ft.
Melee short sword +10 (1d6+1) and
bite +8 (1d4)
Ranged sling +9 (1d4+1)
Space 5 ft; Reach 5 ft.
Base Atk +4; Grp +5
Atk Options sneak attack +2d6
Abilities Str 12, Dex 20, Con 13, Int 11, Wis 13, Cha 12
Feats Acrobatic Strike, Multiattack, Weapon Finesse
Skills: Balance +7, Bluff +9, Diplomacy +5, Disguise +9 (+11 acting), Escape Artist +11, Hide +11, Intimidate +5, Jump +5, Listen +9, Move Silently +11, Spot +9, Tumble +14, Use Rope +5
Possessions: Short sword, sling, 10 bullets, leather armor
Acrobatic Strike: Avoid target's attack of opportunity via tumble, gain +6 on next attack against him.